Journal of Genetics and Genomics

Potential coexistence of both bacterial and eukaryotic small RNA biogenesis and functional related protein homologs in Archaea

Yan Li, Xiuying Liu, Li Huang, Huishan Guo, Xiu-Jie Wang

2010, 37(8): 493-503. doi: 10.1016/S1673-8527(09)60069-2

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Abstract:
RNA silencing plays crucial roles in both bacteria and eukaryotes, yet its machinery appears to differ in these two kingdoms. A couple of Argonaute protein homologs have been reported in some archaeal species in recent years. As Argonaute protein is the key component of eukaryotic RNA silencing pathways, such findings suggested the possibility of existence of eukaryotic RNA silencing like pathways in Archaea, which present the life forms between prokaryotes and eukaryotes. To further explore such hypothesis, we systematically screened 71 fully sequenced archaeal genomes, and identified some proteins containing homologous regions to the functional domains of eukaryotic RNA silencing pathway key proteins. The phylogenetic relationships of these proteins were analyzed. The conserved functional amino acids between archaeal and eukaryotic Piwi domains suggested their functional similarity. Our results provide new clues to the evolution of RNA silencing pathways.

Epistatic effect between ACACA and FABP2 gene on abdominal fat traits in broilers

Guo Hu, Shouzhi Wang, Jianwei Tian, Lili Chu, Hui Li

2010, 37(8): 505-512. doi: 10.1016/S1673-8527(09)60070-9

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Abstract:
Epistasis is generally defined as the interaction between two or more genes or their mRNA or protein products to influence a single trait. Experimental evidence suggested that epistasis could be important in the determination of the genetic architecture of complex traits in domestic animals. Acetyl-coenzyme A carboxylase alpha (ACACA) and fatty acid binding protein 2 (FABP2) are both key factors of lipogenesis and transport. They may play a crucial role in the weight variability of abdominal adipose tissue in the growing chicken. In this study, the polymorphisms of c.2292G>A inACACA and c.-561A>C inFABP2 were detected among individuals from two broiler lines which were divergently selected for abdominal fat content. Epistasis between the two SNPs on abdominal fat weight (AFW) and abdominal fat percentage (AFP) was analyzed. The additive × additive epistatic components between these two SNPs were found significant or suggestively significant on both AFW and AFP in lean lines of the 9th and 10th generation; whereas, it was not significantly associated with either AFW or AFP in fat lines. At the same time, there were not any other significant epistatic components found in both generations or in both lines. Significant epistatic effects between these two SNPs found only in the lean lines could partly be due to the fact that the abdominal fat traits in these two experimental lines have been greatly modified by strong artificial selection. The results suggested that the epistasis mode may be different between the lean and fat chicken lines. Our results could be helpful in further understanding the genetic interaction between candidate genes contributing to phenotypic variation of abdominal fat content in broilers.

Expression of the Tribolium castaneum (Coleoptera: Tenebrionidae) hsp83 gene and its relation to oogenesis during ovarian maturation

Jingjing Xu, Juan Shu, Qin Zhang

2010, 37(8): 513-522. doi: 10.1016/S1673-8527(09)60071-0

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Abstract:
Heat shock proteins (HSP) can protect organisms and cells from thermal damage. In this study, we cloned the full length cDNA encoding the HSP83 protein (the homologue of HSP90) of Tribolium castaneum (red flour beetle). The isolated cDNA contains the full coding sequence, a partial 5′ untranslated region of 55 bp and the complete 3′ untranslated region. We found the hsp83 gene is located on chromosome 5 of the T. castaneum genome. The predicted HSP83 protein sequence has a high similarity (on average 86.77%) with that of other insect species. The expression of the hsp83 gene in the whole body and in the ovary could be induced with heat stress (40° for 1 h) in newly hatched (within 3 h post emergence) and mature (10 days post emergence) beetles. Under normal conditions, the hsp83 expression in the ovary is about 3-fold higher than in the whole body at both stages. No significant difference in hsp83 expression was observed between the two ovarian developmental stages regardless if the beetles were treated with heat shock or not. The expression of the HSP83 protein in the whole body could also be induced with heat stress in newly hatched and mature beetles. However, in the ovary, HSP83 was only expressed in the follicle cells of mature beetles and not in newly hatched beetles, regardless if the beetles were treated with heat shock or not. Furthermore, the females were not able to produce mature oocytes after knock-down of thehsp83 expression by injecting dsRNA. These results suggest that the HSP83 protein is involved in protection against heat stress and could be involved in oogenesis during ovarian maturation of T. castaneum.

Mapping of qGL7-2, a grain length QTL on chromosome 7 of rice

Gaoneng Shao, Shaoqing Tang, Ju Luo, Guiai Jiao, Xiangjin Wei, Ao Tang, Jianli Wu, Jieyun Zhuang, Peisong Hu

2010, 37(8): 523-531. doi: 10.1016/S1673-8527(09)60072-2

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Abstract:
A residual heterozygous line (RHL) carrying a heterozygous segment between two SSR loci RM11 and RM134 on the rice chromosome 7 was selected from a set of recombinant inbred lines from the cross D50 (javanica)/HB277 (indica). The former parent produces much longer grains than the latter. Selfed progenies of this selection were analyzed genotypically (SSRs) and phenotypically (grain length). Grain length was discontinuously variable in the mapping populations, allowing for the placement of this QTL qGL7-2 within a ∼4.8 cM interval defined by RM351 and RM234. A set of new markers within this region were developed, which narrowed the QTL to a 278 kb region defined by the markers Indel1 and RM21945. This region contains 49 predicted genes. The results also suggest that the novel allele for grain length will be used for the application of marker assisted selection for the improvement of grain length.

Novel pleiotropic loci controlling panicle architecture across environments in japonica rice (Oryza sativa L.)

Yuan Guo, Delin Hong

2010, 37(8): 533-544. doi: 10.1016/S1673-8527(09)60073-4

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Abstract:
To identify quantitative trait loci (QTLs) controlling panicle architecture in japonica rice, a genetic map was constructed based on simple sequence repeat (SSR) markers and 254 recombinant inbred lines (RILs) derived from a cross between cultivars Xiushui 79 and C Bao. Seven panicle traits were investigated under three environments. Single marker analysis indicated that a total of 27 SSR markers were highly associated with panicle traits in all the three environments. Percentage of phenotypic variation explained by single locus varied from 2% to 35%. Based on the mixed linear model, a total of 40 additive QTLs for seven panicle traits were detected by composite interval mapping, explaining 1.2%–35% of phenotypic variation. Among the 9 QTLs with more than 10% of explained phenotypic variation, two QTLs were for the number of primary branches per panicle (NPB), two for panicle length (PL), two for spikelet density (SD), one for the number of secondary branches per panicle (NSB), one for secondary branch distribution density (SBD), and one for the number of spikelets per panicle (NS), respectively. qPLSD-9-1 and qPLSD-9-2 were novel pleiotropic loci, showing effects on PL and SD simultaneously. qPLSD-9-1 explained 34.7% of the phenotypic variation for PL and 25.4% of the phenotypic variation for SD, respectively. qPLSD-9-2 explained 34.9% and 24.4% of the phenotypic variation for PL and SD, respectively. The C Bao alleles at the both QTLs showed positive effects on PL, and the Xiushui 79 alleles at the both QTLs showed positive effects on SD. Genetic variation of panicle traits are mainly attributed to additive effects. QTL × environment interactions were not significant for additive QTLs and additive × additive QTL pairs.

Identification of genomic regions determining flower and pod numbers development in soybean (Glycine max L.)

Dan Zhang, Hao Cheng, Hui Wang, Hengyou Zhang, Chunying Liu, Deyue Yu

2010, 37(8): 545-556. doi: 10.1016/S1673-8527(09)60074-6

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Abstract:
Flower and pod numbers per plant are important agronomic traits underlying soybean yield. So far quantitative trait loci (QTL) detected for flower and pod-related traits have mainly focused on the final stage, and might therefore have ignored genetic effects expressed during a specific developmental stage. Here, dynamic expressions of QTL for flower and pod numbers were identified using 152 recombinant inbred lines (RILs) and a linkage map of 306 markers. Wide genetic variation was found among RILs; 17 unconditional and 18 conditional QTL were detected for the two traits at different developmental stages over two years. Some QTL were detected only at one stage and others across two or more stages, indicating that soybean flower and pod numbers development may be governed by time-dependent gene expression. Three main QTL (qfn-Chr18-2, qfn-Chr20-1, and qfn-Chr19) were detected for flower number, and two main QTL (qpn-Chr11 and qpn-Chr20) were detected for pod number. The phenotypic variation explained by them ranged from 6.1% to 34.7%. The markers linked to these QTL could be used in marker-assisted selection for increasing soybean flower and pod numbers, with the ultimate aim of increasing soybean yield. Comparison of the QTL regions for flower and pod numbers traits with the related genes reported previously showed that seven and four related genes were located in the QTL regions of qfn-Chr11 and qfn-Chr19, respectively. These results provide a basis for fine mapping and cloning of flower and pod development-related genes.

2010 Vol. 37, No. 8