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28 December 2008, Volume 15 Issue 4 Previous Issue    Next Issue
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InDel and SNP Markers and Their Applications in Map-based Cloning of Rice Genes PAN Cun-hong, LI Ai-hong, DAI Zheng-yuan, ZHANG Hong-xi, LIU Guang-qing, WANG Zi-bin, MA Yu-yin, YIN Yue-jun, ZHANG Ya-fang, ZUO Shi-min, CHEN Zong-xiang, PAN Xue-biao 2008, 15(4): 251-258 .  Abstract ( )   PDF   High-density markers are necessary for map-based cloning of rice genes, but the currently available markers are not satisfactory enough. InDel (insertion-deletion length polymorphism) and SNP (single nucleotide polymorphism) are the new generation of molecular markers and can basically meet the need of fine mapping. InDel and SNP markers can be developed through bioinformatics. These markers are valuable markers with the characters of low cost, high specificity and stability. This article introduced the methods for designing InDel and SNP markers, taking the mapping of a rice rolled leaf gene as an example. In addition, some key factors in improving the design efficiency were also discussed.

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Dissection of QTLs for Yield Traits Using Near Isogenic Lines Derived from Residual Heterozygous Lines in Rice DU Jing-hong, FAN Ye-yang, WANG Lei, ZHUANG Jie-yun 2008, 15(4): 259-266 .  Abstract ( )   PDF   Three residual heterozygous lines (RHLs) carrying heterozygous segments in the intervals RM587–RM225, RM204–RM6119 and RM6119–RM402 on the short arm of rice chromosome 6, respectively, were selected from a rice population derived from an RHL for the interval RM587–RM402. Ten maternal homozygotes, 10 paternal homozygotes and 20 heterozygotes were selected from each of the F2 populations derived from the three RHLs. The three sets of near isogenic lines (NILs) were grown to detect the grain yield per plant, number of panicles per plant, number of filled grains per panicle and 1000-grain weight. With analysis on the phenotypic differences among the three genotype groups in each NIL set and those among overlapping chromosome segment substitution lines, three QTLs for number of filled grains per panicle and two QTLs for grain yield per plant were resolved. They were located in the intervals ranging from 0.66 Mb to 2.49 Mb. The additive effect was higher than the dominance effect at each locus. The allele for increasing the trait value was derived from the paternal parent at qNFGP6-1, and from the maternal alleles at other QTLs. Based on the present study, an approach for constructing new genetic resource to facilitate fine mapping of QTLs in rice was proposed.

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Distribution Characterization of Leaf and Hull Pubescences and Genetic Analysis of Their Numbers in japonica Rice (Oryza sativa) ZHU Xiao-biao, SUN Da-yun, CHENG Bao-shan, HONG De-lin 2008, 15(4): 267-275 .  Abstract ( )   PDF   Distributions of pubescences on leaf blade and hull in japonica rice were observed under an optical microscope. Numbers of leaf and hull pubescences in P1, P2, F1, B1, B2 and F2 generations were investigated in three combinations of japonica rice (Sidao 10A/Wuyujing 3R, Wuyujing 3A/Sidao 10R and Liuyan 189A/HR-122), and genetic analysis for these two traits were conducted by using the joint analysis method of P1, P2, F1, B1, B2 and F2 generations with the mixed major gene plus polygene inheritance models. Leaf pubescences characterized by swollen base and fine tip distributed regularly on the boundary between dark green stripe and light green stripe of leaf blade. Hull pubescences with various lengths distributed irregularly on the whole hull. Numbers of leaf pubescences in the reciprocal combinations of Sidao 10A/Wuyujing 3R and Wuyujing 3A/Sidao 10R and numbers of hull pubescences in all the three combinations were controlled by one pair of additive major genes plus additive-dominant polygenes. In the combination of Liuyan 189A/HR-122, number of leaf pubescences was controlled by one pair of additive-dominant major genes plus additive-dominant polygenes. Both numbers of leaf and hull pubescences were mainly governed by major genes.

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Role of LOX3 Gene in Alleviating Adverse Effects of Drought and Pathogens in Rice LIU Nan-nan, JIANG Ling, ZHANG Wen-wei, LIU Ling-long, ZHAI Hu-qu, WAN Jian-min, 2008, 15(4): 276-282 .  Abstract ( )   PDF   Lipoxygenase 3 (LOX3) is a major component of the LOX isozymes in mature rice seeds. To investigate the role of LOX3 gene under stresses, a plant expression vector containing antisense cDNA of LOX3 was constructed. Rice varieties Wuyunjing 7 and Kasalath were transformed by the Agrobacterium-mediated method and transgenic rice plants were generated. PCR and Southern blot results showed that the antisense LOX3 gene was integrated into the rice genome. Analyses of embryo LOX3 deletion and semi-quantitative RT-PCR confirmed the antisense suppression of LOX3 gene in transgenic plants. The T2 antisense plants of LOX3 were sensitive to drought stress, rice blast and bacterial blight compared with non-transgenic plants. These results suggest that the LOX3 gene might function in response to stresses.

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Molecular Cytogenetic Analysis of Spontaneous Interspecific Hybrid Between Oryza sativa and Oryza minuta YI Chuan-deng, CHENG Xu, WANG Bei-bei, LIANG Guo-hua, GONG Zhi-yun, TANG Shu-zhu, GU Ming-hong 2008, 15(4): 283-288 .  Abstract ( )   PDF   Genomic in situ hybridization (GISH) is a powerful tool to characterize parental chromosomes in interspecific hybrids, including the behaviour of autosynapsis and chromosome pairing. It was used to distinguish the chromosomes of Oryza sativa from wild species in a spontaneous interspecific hybrid and to investigate the chromosome pairing at metaphase I in meiosis of the hybrid in this study. The hybrid was a triploid with 36 chromosomes according to the chromosome number investigated in mitosis of root tips. During metaphase I of meiosis in the hybrid, less chromosome pairing was observed and most of the chromosomes existed as univalent. Based on GISH and FISH (Fluorescent in situ hybridization) analyses, the chromosomes of the hybrid were composed of genomes A, B and C. Thus, it was believed that the hybrid was the result of natural hybridization between cultivated rice and wild species O. minuta which was planted in experimental fields.

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SSR Analysis on Diversity of AA Genome Oryza Species in the Southeast and South Asia LU Jian-zhen, ZHANG Xiao-li, WANG Hai-gang, YUAN Xiao-ping, XU Qun, WANG Yi-ping, YU Han-yong, TANG Sheng-xiang, WEI Xing-hua 2008, 15(4): 289-294 .  Abstract ( )   PDF   To investigate genetic diversities among the AA genome Oryza species in the Southeast and South Asia, a total of 428 accessions of the AA genome Oryza species were genotyped using 36 simple sequence repeats (SSR) markers distributed throughout the rice genome. All of the 36 SSR markers generated polymorphic bands, revealing 100% polymorphism. The number of alleles per locus ranged from 3 to 17 with the mean of 8.6. The Nei’s genetic diversity index (He) ranged from 0.337 at RM455 to 0.865 at RM169 with an average value of 0.650. The genetic diversity of the AA genome Oryza species in the Southeast Asia was obviously higher than that in the South Asia. Among the detected Oryza species in the South and Southeast Asia, O. rufipogon showed the highest genetic diversity. Meanwhile, a higher genetic differentiation (Fst) was found among the detected Oryza species in the Southeast Asia than in the South Asia. The Fst value between O. nivara and O. sativa was the highest. The results from the number of specific alleles, specific loci, and allele frequency confirmed the greater genetic variation among the detected species. In addition, the specific allele in RM161 displayed higher frequency (0.193), suggesting its important function in identifying Oryza species of AA genome.

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Genetic Diversity and Relationship of Weedy Rice in Taizhou City, Jiangsu Province, China ZHANG Juan, Nilda R. BURGOS, MA Kun, ZHOU Yong-jun, GENG Rui-mei, YU Liu-qing 2008, 15(4): 295-302 .  Abstract ( )   PDF   Microsatellite markers and morphological characteristics were used to explore the genetic diversity and possible origin of weedy rice in Taizhou City, Jiangsu Province, China. Fifty-two weedy rice (Oryza sativa L.) accessions were compared with two wild rice, four hybrid rice and five cultivars using 22 simple sequence repeat (SSR) primer pairs. A total of 107 fragments were amplified, averaging 5.6 alleles per primer pair. The polymorphic index content (PIC) values ranged from 0.3077 to 0.7951, averaging at 0.5870. The average genetic distance of all samples ranged from 0.02 to 0.46 with an average of 0.262. The genetic distance among Taizhou weedy rice ranged from 0.03 to 0.44 with an average of 0.224. Cluster analysis showed that all the weedy rice accessions from Taizhou City were indica, and could be subdivided into different genotypes. The majority (86%) of weedy rice was most closely related to hybrid rice. The Taizhou weedy rice accessions were morphologically similar, but still could be delineated into indica or japonica group by some morphological traits. It is suggested that the levels of genetic and morphological diversities of weedy rice in Taizhou City are low and these weedy rice plants originated from the segregating progenies of hybrid rice that had naturally introgressed with cultivated rice.

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Use of Selection Indices Based on Multivariate Analysis for Improving Grain Yield in Rice Hossein SABOURI, Babak RABIEI, Maryam FAZLALIPOUR 2008, 15(4): 303-310 .  Abstract ( )   PDF   In order to study selection indices for improving rice grain yield, a cross was made between an Iranian traditional rice (Oryza sativa L.) variety, Tarommahalli and an improved indica rice variety, Khazar in 2006. The traits of the parents (30 plants), F1 (30 plants) and F2 generations (492 individuals) were evaluated at the Rice Research Institute of Iran (RRII) during 2007. Heritabilities of the number of panicles per plant, plant height, days to heading and panicle exsertion were greater than that of grain yield. The selection indices were developed using the results of multivariate analysis. To evaluate selection strategies to maximize grain yield, 14 selection indices were calculated based on two methods (optimum and base) and combinations of 12 traits with various economic weights. Results of selection indices showed that selection for grain weight, number of panicles per plant and panicle length by using their phenotypic and/or genotypic direct effects (path coefficient) as economic weights should serve as an effective selection criterion for using either the optimum or base index.

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Race Specificity of Major Rice Blast Resistance Genes to Magnaporthe grisea Isolates Collected from indica Rice in Guangdong, China YANG Jian-yuan, CHEN Shen, ZENG Lie-xian, LI Yi-long, CHEN Zhen, LI Chuan-ying, ZHU Xiao-yuan 2008, 15(4): 311-318 .  Abstract ( )   PDF   Race-specific resistance and field resistance of 30 rice blast resistance monogenic lines derived from different resources were evaluated. The spectra of resistance to 163 Magnaporthe grisea isolates collected from indica rice in Guangdong Province, China ranged from 0.6% to 89.6%. Most of the monogenic lines showed a narrow resistance spectrum and high susceptibility in rice blast area, whereas the lines with Pikh and Pi1(t) had the broad resistance spectra of 89.6% and 82.2% respectively, showing a high and stable blast resistance in fields. According to the cluster analysis of specific resistance to 163 blast isolates tested, the 30 monogenic lines were divided into 15 groups, and based on the principal factor analysis, nine kinds of race-specific resistance were identified. Pik, Piz5, Pi9 and Pish can be used as candidate resistance genes for rice breeding since their specific resistance differed from those of the backbone parents in Guangdong, China. Gene pyramiding of Pikh [or Pi1(t)], Pi9 (or Piz5) and Pish (or Pita2) will be effective to obtain broad-spectrum blast resistance in rice breeding program in Guangdong, China. The strategies for studying and application of rice blast resistance genes were discussed.

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Effects of Cadmium Stress on Seed Germination, Seedling Growth and Seed Amylase Activities in Rice (Oryza sativa) HE Jun-yu, REN Yan-fang, ZHU Cheng, JIANG De-an 2008, 15(4): 319-325 .  Abstract ( )   PDF   Two rice varieties, Xiushui 110 with high cadmium (Cd) tolerance and Xiushui 11 with low Cd tolerance were used to study the effects of Cd stress on seed germination, seedling growth and amylase activities. The low cadmium concentration had little effect on seed germination rate. However, cadmium stress could significantly inhibit plumule and radicle growth, especially for radicle growth. Germination index, vigour index, radicle length and amylase activities of Xiushui 11 decreased more significantly with the increasing cadmium level compared with Xiushui 110. The cadmium content in seedlings of Xiushui 11 was higher than that in Xiushui 110 when the cadmium concentration exceeded 5 μmol/L, which caused lower mitotic index in root tips and amylase activities, and more serious cadmium toxicity in Xiushui 11.

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High Temperature Effects on Yeast-like Endosymbiotes and Pesticide Resistance of the Small Brown Planthopper, Laodelphax striatellus ZHANG Xiao-jie, YU Xiao-ping, CHEN Jian-ming 2008, 15(4): 326-330 .  Abstract ( )   PDF   The newly-hatched nymphs of the small brown planthopper (SBPH), Laodelphax striatellus, including field and sensitive populations, were subjected to the high-temperature (35°C) treatment. The number of yeast-like endosymbiotes in SBPH reduced by 23.47%–34.23%, 57.86%–61.51% and 88.96%–90.71% after the high-temperature treatment for 1 d, 2 d, and 3 d, respectively. However, the size of yeast-like endosymbiotes was not obviously affected. Resistance of SBPH to three insecticides (imidacloprid, chlorpyrifos and fipronil) decreased with the increase of treatment time.