28 January 2013, Volume 20 Issue 1 Previous Issue    Next Issue

    Review or Special Topic
    Research Paper
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    Review or Special Topic
    Quantitative Trait Loci for Heading Date and Their Relationship with Genetic Control of Yield Traits in Rice (Oryza sativa)
    GUO Liang, ZHANG Zhen-hua, ZHUANG Jie-yun
    2013, 20(1): 1-12.  DOI: 10.1016/S1672-6308(13)60101-8
    Abstract ( )   PDF (198KB) ( )  

    Grain yield and heading date are key factors determining the commercial potential of a rice variety. Mapping of quantitative trait loci (QTLs) in rice has been advanced from primary mapping to gene cloning, and heading date and yield traits have always attracted the greatest attention. In this review, genomic distribution of QTLs for heading date detected in populations derived from intra-specific crosses of Asian cultivated rice (Oryza sativa) was summarized, and their relationship with the genetic control of yield traits was analyzed. The information could be useful in the identification of QTLs for heading date and yield traits that are promising for the improvement of rice varieties.

    Research Paper
    Genetic Analysis and Gene Mapping of Light Brown Spotted Leaf Mutant in Rice
    FENG Bao-hua1, YANG Yang1, 2, SHI Yong-feng1, LIN Lu3, CHEN Jie1, WEI Yan-lin1, 2, Hei LEUNG4, WU Jian-li1
    2013, 20(1): 13-18.  DOI: 10.1016/S1672-6308(13)60102-X
    Abstract ( )   PDF (203KB) ( )  

    A light brown spotted-leaf mutant of rice was isolated from an ethane methyl sulfonate (EMS)- induced IR64 mutant bank. The mutant, designated as lbsl1 (light brown spotted-leaf 1), displayed light brown spot in the whole growth period from the first leaf to the flag leaf under natural summer field conditions. Agronomic traits including plant height, growth duration, number of filled grains per panicle, seed-setting rate and 1000-grain weight of the mutant were significantly affected. Genetic analysis showed that the mutation was controlled by a single recessive gene, tentatively named lbsl1(t), which was mapped to the short arm of chromosome 6. By developing simple sequence repeat (SSR) markers, the gene was finally delimited to an interval of 130 kb between markers RM586 and RM588. The lbsl1(t) gene is likely a novel rice spotted-leaf gene since no other similar genes have been identified near the chromosomal region. The genetic data and recombination populations provided will facilitate further fine-mapping and cloning of the gene.

    Breeding and Identification of Insect-Resistant Rice by Transferring Two Insecticidal Genes, sbk and sck
    ZHANG Qi-jun, LI Cong, LIU Shao-kui, LAI Dong, QI Qing-ming, LU Chuan-gen
    2013, 20(1): 19-24.  DOI: 10.1016/S1672-6308(13)60103-1
    Abstract ( )   PDF (386KB) ( )  

    The plasmid of pCDMARUBA-Hyg, which contained two insect-resistance genes, sbk (modified from Cry1A(c)) and sck (modified from CpTI), was transformed into an Agrobacterium EHA105 for infection of the calli of a super japonica rice Nanjing 45. Primarily, using polymerase chain reaction (PCR) detection with the primers of sbk and sck genes, 42 positive transgenic plants that were marker-free and contained the two target genes were selected from 97 regenerated plants. Results of southern-blotting indicated that 23, 11, 5, 2 and 1 plants had one, two, three, four and five copies of the transformed genes, respectively. Analysis of reverse transcription PCR (RT-PCR) and Bt gene testing paper showed that 28 T3 generation plants derived from four transgenic plants having a single copy were insect-resistant. Feeding experiment with rice stem borer revealed that the insect resistance was greatly increased with the larva mortality ranging from 94% to 100%. In addition, among the transgenic plants, three T3 transgenic plants possessed some desirable characteristics for breeding and production, such as plant height, seed-setting rate, 1000-grain weight and larva mortality. The mechanism of insect resistance of Bt gene and its application in rice transgenic research were also briefly discussed.

    Evaluation and Bulked Segregant Analysis of Major Yield QTL qtl12.1 Introgressed into Indigenous Elite Line for Low Water Availability under Water Stress
    N. Manikanda BOOPATHI1, Gat SWAPNASHRI1, P. KAVITHA1, S. SATHISH1, R. NITHYA1, Wickneswari RATNAM2, Arvind KUMAR3
    2013, 20(1): 25-30.  DOI: 10.1016/S1672-6308(13)60104-3
    Abstract ( )   PDF (282KB) ( )  

    Near isogenic lines carrying large-effect QTL (qtl12.1), which has a consistent influence on grain yield under upland drought stress conditions in a wide range of environments, were evaluated under water stress in the fields. The line which gave higher yield under drought was crossed with a local elite line, PMK3, and forwarded to F2:3 generation. Significant variation was found among the F2:3 lines for agronomic traits under water stress in the fields. Low to high broad sense heritability (H) for investigated traits was also found. Water stress indicators such as leaf rolling and leaf drying were negatively correlated with plant height, biomass and grain yield under stress. Bulked segregant analysis (BSA) was performed with the markers in the vicinity of qtl12.1, and RM27933 was found to be segregated perfectly well in individual components of drought resistant and drought susceptible bulks which were bulked based on yield under water stress among F2:3 lines. Hence, this simple and breeder friendly marker, RM27933, may be useful as a potentially valuable candidate marker for the transfer of the QTL qtl12.1 in the regional breeding program. Bioinformatic analysis of the DNA sequence of the qtl12.1 region was also done to identify and analyze positional candidate genes associated with this QTL and to ascertain the putative molecular basis of qtl12.1.

    QTL Analysis for Seven Quality Traits of RIL Population in Japonica Rice Based on Three Genetic Statistical Models
    LIU Qiang-ming1, JIANG Jian-hua1, 2, NIU Fu-an1, HE Ying-jun1, HONG De-lin1
    2013, 20(1): 31-38.  DOI: 10.1016/S1672-6308(13)60105-5
    Abstract ( )   PDF (348KB) ( )  

    QTL mapping for seven quality traits was conducted by using 254 recombinant inbred lines (RIL) derived from a japonica-japonica rice cross of Xiushui 79/C Bao. The seven traits investigated were grain length (GL), grain length to width ratio (LWR), chalk grain rate (CGR), chalkiness degree (CD), gelatinization temperature (GT), amylose content (AC) and gel consistency (GC) of head rice. Three mapping methods employed were composite interval mapping in QTLMapper 2.0 software based on mixed linear model (MCIM), inclusive composite interval mapping in QTL IciMapping 3.0 software based on stepwise regression linear model (ICIM) and multiple interval mapping with regression forward selection in Windows QTL Cartographer 2.5 based on multiple regression analysis (MIMR). Results showed that five QTLs with additive effect (A-QTLs) were detected by all the three methods simultaneously, two by two methods simultaneously, and 23 by only one method. Five A-QTLs were detected by MCIM, nine by ICIM and 28 by MIMR. The contribution rates of single A-QTL ranged from 0.89% to 38.07%. All the QTLs with epistatic effect (E-QTLs) detected by MIMR were not detected by the other two methods. Fourteen pairs of E-QTLs were detected by both MCIM and ICIM, and 142 pairs of E-QTLs were detected by only one method. Twenty-five pairs of E-QTLs were detected by MCIM, 141 pairs by ICIM and four pairs by MIMR. The contribution rates of single pair of E-QTL were from 2.60% to 23.78%. In the Xiu-Bao RIL population, epistatic effect played a major role in the variation of GL and CD, and additive effect was the dominant in the variation of LWR, while both epistatic effect and additive effect had equal importance in the variation of CGR, AC, GT and GC. QTLs detected by two or more methods simultaneously were highly reliable, and could be applied to improve the quality traits in japonica hybrid rice.

    Genetic Structure and Indica/Japonica Component Changes in Major Inbred Rice Varieties in China
    YU Ping, YUAN Xiao-ping, XU Qun, WANG Cai-hong, YU Han-yong, WANG Yi-ping,TANG Sheng-xiang, WEI Xing-hua
    2013, 20(1): 39-44.  DOI: 10.1016/S1672-6308(13)60104-3
    Abstract ( )   PDF (802KB) ( )  

    We used 39 SSR markers to analyze the genetic structure of 304 major Chinese inbred rice varieties, and to compare changes in the indica or japonica components in these varieties that have been widely cultivated from the 1950s to the 1990s in China. The genetic structure analysis showed that these rice varieties were distinctly divided into two populations, indica and japonica. The sub-structure of indica varieties was more complex than that of japonica ones. Among the various lines, late-season indica and early season japonica varieties had simpler genetic backgrounds. The seasonal ecotypes were not quite consistent with the subtypes of genetic structure. Twelve SSR loci with specific differentiation between indica and japonica were used to calculate the indica/japonica components. The differences in indica/japonica components among the five decades were not significant, except for late-season indica varieties in the 1990s, which had a significantly higher japonica component. These results will help to understand the genetic structure of the major Chinese inbred rice varieties and will be useful for indica-japonica hybrid breeding in China.

    Parental Selection in Rice Cultivar Improvement
    Stanley Omar P B. Samonte1, Rodante E. Tabien2, Lloyd T. Wilson2
    2013, 20(1): 45-51.  DOI: 10.1016/S1672-6308(13)60107-9
    Abstract ( )   PDF (200KB) ( )  

    The evaluation of rice (Oryza sativa L.) cultivars assists breeders in identifying useful trait relationships and in selecting parents as donors of specific traits. This study was conducted to compare long-grain rice cultivars using genotype × trait (GT) biplot analysis and determine potential donors of traits related to grain yield and quality. Seventeen cultivars in the 2005 and 2006 Uniform Regional Rice Nursery in Beaumont, Texas, USA were analyzed for 20 traits using GT biplot analysis. The GT biplots showed the diversity among cultivars with regards to yield-related traits. Cultivars recommended as donor parents were: Trenasse, Spring, Presidio, and Cocodrie for high grain yield and head rice rate; Trenasse and Presidio for semi-dwarfness; Banks for tall plant height; Wells for high flag leaf area, panicle weight, and number and mass of filled grains per panicle; Hidalgo for high tiller density; Francis for high number of spikelets per panicle; Spring and Trenasse for short flowering duration; Cheniere for more days to heading and maturity and Spring for less days; and Spring and Hidalgo for high grain weight. Breeders can use these cultivars with specific traits to increase grain yield and quality.

    Water, Nitrogen and Plant Density Affect the Response of Leaf Appearance of Direct Seeded Rice to Thermal Time
    Maite MARTíNEZ-EIXARCH 1, *, ZHU De-feng2, CATALà-FORNER Maria del Mar1, PLA-MAYOR Eva1, TOMáS-NAVARRO Nuria1
    2013, 20(1): 52-60.  DOI: 10.1016/S1672-6308(13)60108-0
    Abstract ( )   PDF (374KB) ( )  

    Field experiments were conducted in the Ebro Delta area (Spain), from 2007 to 2009 with two rice varieties: Gleva and Tebre. The experimental treatments included a series of seed rates, two different water management systems and two different nitrogen fertilization times. The number of leaves on the main stems and their emergence time were periodically tagged. The results indicated that the final leaf number on the main stems in the two rice varieties was quite stable over a three-year period despite of the differences in their respective growth cycles. Interaction between nitrogen fertilization and water management influenced the final leaf number on the main stems. Plant density also had a significant influence on the rate of leaf appearance by extending the phyllochron and postponing the onset of intraspecific competition after the emergence of the 7th leaf on the main stems. Final leaf number on the main stems was negatively related to plant density. A relationship between leaf appearance and thermal time was established with a strong nonlinear function. In direct-seeded rice, the length of the phyllochron increases exponentially in line with the advance of plant development. A general model, derived from 2-year experimental data, was developed and satisfactorily validated; it had a root mean square error of 0.3 leaf. An exponential model can be used to predict leaf emergence in direct-seeded rice.

    Effect of Phosphorus and Irrigation Levels on Yield, Water Productivity, Phosphorus Use Efficiency and Income of Lowland Rice in Northwest Pakistan
    Khalid USMAN
    2013, 20(1): 61-72.  DOI: 10.1016/S1672-6308(13)60109-2
    Abstract ( )   PDF (205KB) ( )  

    With decreasing availability of water for agriculture and increasing demand for rice production, an optimum use of irrigation water and phosphorus may guarantee sustainable rice production. Field experiments were conducted in 2003 and 2004 to investigate the effect of phosphorus and irrigation levels on yield, water productivity (WP), phosphorus use efficiency (PUE) and income of low land rice. The experiment was laid out in randomized complete block design with split plot arrangements replicated four times. Main plot consisted of five phosphorus levels, viz. 0 (P0), 50 (P50), 100 (P100), 150 (P150), and 200 (P200) kg/hm2, while subplots contained of irrigation times, i.e. 8 (I8), 10 (I10), 12 (I12), and 14 (I14) irrigation levels, each with a water depth of 7.5 cm. Mean values revealed that P150 in combination with I10 produced the highest paddy yield (9.8 t/hm2) and net benefit (1 231.8 US$/hm2) among all the treatments. Phosphorus enhanced WP when applied in appropriate combination with irrigation level. The highest mean WP [13.3 kg/(hm2?mm)] could be achieved at P150 with I8 and decreased with increase in irrigation level, while the highest mean PUE (20.1 kg/kg) could be achieved at P100 with I10 and diminished with higher P levels. The overall results indicate that P150 along with I10 was the best combination for sustainable rice cultivation in silty clay soil.

    Identification and Genetic Analysis of Gall Midge Resistance in Rice Germplasm 91-1A2
    LU Jia-shi1, 2, HE Long-fei1, XU Jing1, XU Chun-yan1, LI Chuang-zhen1, WEI Su-mei3, SU Jian-mu1
    2013, 20(1): 73-78.  DOI: 10.1016/S1672-6308(13)60110-9
    Abstract ( )   PDF (199KB) ( )  

    Resistance to rice gall midge in rice germplasm 91-1A2 was identified and genetically analyzed. F1s of rice population were derived from 91-1A2 which crossed with rice materials Jinggui, TN1, W1263 (Gm1), IET2911 (Gm2), BG404-1 (gm3), OB677 (Gm4), ARC5984 (Gm5) and Duokang 1 (Gm6) as a male parent. The resistance of all parental lines and F1, BC1F1 and F2 populations to rice gall midge was identified. The results showed that 91-1A2 and all F1s were resistant to Chinese rice gall midge biotype IV. The segregation ratio of resistant plants to susceptible ones in BC1F1 and F2 were accorded with 1:3 and 9:7 rules by χ2 test, suggesting that the resistance of 91-1A2 to Chinese rice gall midge biotype IV was controlled by two dominant genes which were new resistance genes, non-allelic to the known rice gall midge resistance genes.