Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon (original) (raw)
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Interaction of Rice Quantitative Trait Locusgw9.1 with Three Grain Shape Genes
Plant Breeding and Biotechnology
Grain size is one of the most important factors determining grain yield in rice breeding. In previous studies, we constructed high-density maps for two quantitative trait loci (QTL) for grain weight, tgw2 and gw9.1, using progeny derived from crosses between the japonica cultivar Hwaseong and Oryza grandiglumis, and Hwaseong and O. rufipogon (IRGC 105491), respectively. The wild alleles contributed an increase in grain weight at these two loci. We developed an F2 population (146 plants) by crossing two near isogenic lines (NILs) harboring tgw2 and gw9.1 to know how they interact in the near isogenic background. Simple sequence repeat markers tightly linked to two QTL were used to check the genotype of the F2 population. Based on the genotype at two loci, 146 F2 plants were classified into 9 groups with a combination of three genotypes at each two loci. Two gene interaction was not significant (P=0.99) in the F2. Homozygous plants with wild alleles at two loci showed significantly higher 1,000 grain weight than plants with a single QTL in the F2 and F3. These results indicate that two QTLs act additively in distinct or complementary pathways in controlling GW. Gene expression analysis was also performed to know the relationship of the gw9.1 QTL with three major grain size genes with Hwaseong and two NILs plants at the transcription level. The results from this study provide insight into grain size regulation in rice and are likely to be useful for marker aided selection for grain size.
Genetics and Molecular Research, 2014
M.S. Ngu et al. and RM19271.1. According to the Duncan multiple range test, 8 BC 4 F 4 near isogenic lines had significantly higher 100-grain weight (4.8 to 7.5% over MR219) than their recurrent parent, MR219 (P < 0.05). According to the rice genome automated annotation database, there are 20 predicted genes in the 88-kb target region, and 9 of them have known functions. Among the genes with known functions in the target region, in silico gene expression analysis showed that 9 were differentially expressed during the seed development stage(s) from gene expression series GSE6893; however, only 3 of them have known functions. These candidates provide targets for further characterization of qGW6, which will assist in understanding the genetic control of grain weight in rice.
2010
Background: The three-dimensional shape of grain, measured as grain length, width, and thickness (GL, GW, and GT), is one of the most important components of grain appearance in rice. Determining the genetic basis of variations in grain shape could facilitate efficient improvements in grain appearance. In this study, an F 7:8 recombinant inbred line population (RIL) derived from a cross between indica and japonica cultivars (Nanyangzhan and Chuan7) contrasting in grain size was used for quantitative trait locus (QTL) mapping. A genetic linkage map was constructed with 164 simple sequence repeat (SSR) markers. The major aim of this study was to detect a QTL for grain shape and to fine map a minor QTL, qGL7. Results: Four QTLs for GL were detected on chromosomes 3 and 7, and 10 QTLs for GW and 9 QTLs for GT were identified on chromosomes 2, 3, 5, 7, 9 and 10, respectively. A total of 28 QTLs were identified, of which several are reported for the first time; four major QTLs and six minor QTLs for grain shape were also commonly detected in both years. The minor QTL, qGL7, exhibited pleiotropic effects on GL, GW, GT, 1000-grain weight (TGW), and spikelets per panicle (SPP) and was further validated in a near isogenic F 2 population (NIL-F 2). Finally, qGL7 was narrowed down to an interval between InDel marker RID711 and SSR marker RM6389, covering a 258-kb region in the Nipponbare genome, and cosegregated with InDel markers RID710 and RID76. Conclusion: Materials with very different phenotypes were used to develop mapping populations to detect QTLs because of their complex genetic background. Progeny tests proved that the minor QTL, qGL7, could display a single mendelian characteristic. Therefore, we suggested that minor QTLs for traits with high heritability could be isolated using a map-based cloning strategy in a large NIL-F 2 population. In addition, combinations of different QTLs produced diverse grain shapes, which provide the ability to breed more varieties of rice to satisfy consumer preferences.
Scientific Reports, 2021
Grain size and weight are the key traits determining rice quality and yield and are mainly controlled by quantitative trait loci (QTL). In this study, one minor QTL that was previously mapped in the marker interval of JD1009-JD1019 using the Huanghuazhan/Jizi1560 (HHZ/JZ1560) recombinant inbred line (RIL) population, qTGW1-2, was validated to regulate grain size and weight across four rice-growing seasons using twenty-one near isogenic line (NIL)-F2 populations. The twenty-one populations were in two types of genetic background that were derived from the same parents HHZ and JZ1560. Twelve F9, F10 or F11 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were developed from one residual heterozygote (RH) in the HHZ/JZ1560 RIL population, and the remaining nine BC3F3, BC3F4 or BC3F5 NIL-F2 populations with the sequential residual heterozygous regions covering JD1009-RM6840 were constructed through consecutive backcrosses to the recurrent paren...
Genetic Mapping of QTLs that Control Grain Characteristics in Rice (Oryza sativa L.)
Journal of Life Science, 2015
We performed a molecular marker-based analysis of quantitative trait loci (QTLs) for traits that determine the quality of the appearance of grains, using 120 doubled-haploid (DH) lines developed by another culture from the F1 cross between 'Cheongcheong' (Oryza sativa L. ssp. Indica) and 'Nagdong' (Oryza sativa L. ssp. Japonica). The traits studied included length, width, and thickness of the grains, as well as length-to-width ratio and 1,000-grain weight. The objective of this study was to determine the genetic control of these traits in order to formulate a strategy for improving the appearance of this hybrid. Within the DH population, five traits exhibited wide variation, with mean values occurring within the range of the two parents. Three QTLs were identified for grain length on chromosomes 2, 5, and 7. Three QTLs were mapped for grain width on chromosome 2: qGW2-1, qGW2-2, and qGW2-3. Six chromosomes were identified for the grain length-to-width ratio; four of these were on chromosome 2, whereas the other two were on chromosomes 7 and 12. One QTL influencing 1,000-grain weight was identified and located on chromosome 8. The results presented in the present study should facilitate rice-breeding, especially for improved hybrid-rice quality.
Biosciences, Biotechnology Research Asia
With the substantial increase in food grain production, much of the emphasis has been put for enhanced grain quality traits. Most of the grain qualities traits are polygenic in nature. Identification of QTLs and markers linked to these QTLs can substantially enhance the selection efficiency. In this study, an effort has been made to identify QTLs for these traits. For this purpose two mapping population, RIL Safri17 x Kranti and DH population CT-993-5-10-1-M and IR 62266-42-6-2 were used and evaluated under field conditions. DNA from 112 lines of RIL was extracted, quantified and diluted to the appropriate concentration for PCR-based amplification. Fifty markers were used for detecting parental polymorphism. Five markers exhibiting polymorphism were further used for developing marker profile on the complete set of RIL. This data along with genotyping data for this population was used for QTLs analysis using single marker 't' test. RM 110, RM 202 and RM 212 were associated with grain length, RM 84 and RM 539 was associated with grain width, and RM 163, RM 202, RM 247 and RM 80 were associated to be L/B ratio. For DH population MAPMAKER/ QTL 1.1 was used for interval mapping and to estimate the percentage of total phenotypic variation. A threshold of LOD> 2.4 was used per test to claim the presence of QTL. A total of 8 QTLs were detected for grain width and grain L/B ratio. For grain width 3 QTLs detected on chromosome number 2, 3, 6 which shows 11 percent phenotyping variation. For L/B ratio 5 QTLs were detected, which were present on chromosome 2 3, 6 having 9 to 12.5 percent phenotypic variation. For grain length no QTLS detected.
plants, 2024
Grain yield of rice consists of sink capacity and grain filling. There are some genes known to contribute to sink capacity, but few genes associated with grain filling are known. We conducted a genetic analysis on yield-related traits by using a chromosome segment substitution line population that have introgression from DV85, an aus variety of rice, in the background of T65, a japonica variety. Refined whole-genome genotypes of the 43 TD-CSSLs were obtained by genotyping-by-sequencing. The effects of previously detected quantitative trait loci (QTLs), qNSC1 and qNSC2, were confirmed by the amount of non-structural carbohydrate (NSC) at 5 days after heading (DAH). The CSSL for qSWTR11, the QTL for decrease in shoot weight during the maturity stage, showed the highest NSC at 5 DAH and lowest at 35 DAH. The brown rice yield of these lines were not stably significant. Most of the sink-related traits correlated between the 2 tested years, but most of the grain-filling traits did not show correlation between the 2 years. Correlation analysis revealed that the sink capacity is stable and primarily determines the yield, and grain filling is more affected by the environment. In addition, biomass production before heading and during the maturity stage contributes to higher yield in TD-CSSLs, and the amount of translocation of stem reserve does not affect much to the yield. We conclude that higher NSC at the heading stage and rapid decrease in shoot biomass during the maturity stage did not directly contribute to the yield formation in the japonica genetic background.
2011
In our previous study, we reported the grain weight (GW) QTL, tgw11 in isogenic lines derived from a cross between Oryza sativa ssp. Japonica cv. Hwaseong and O. grandiglumis. The O. grandiglumis allele at tgw11 decreased GW in the Hwaseong background. To fine-map tgw11, one F5 plant homozygous for the O. grandiglumis DNA in the target region on chromosome 11 was selected from F4 line, CR1242 segregating for tgw11 and crossed with Hwaseong to produce secondary F2 and F3 populations. QTL analysis using 760 F2 plants confirmed the existence of tgw11 with an R 2 value of 15.0%. This QTL explained 32.2% of the phenotypic variance for GW in 91 F3 lines. Substitution mapping with 65 F3 lines with informative recombination breakpoints in the target region was carried out to narrow down the position of the tgw11. The result indicated that tgw11 was located in the 900-kb interval between two SSR markers, RM224 and RM27358. QTLs for grain width and grain thickness were also located in the same interval suggesting that a single gene is involved in controlling these three traits. Analysis of F3 lines indicated that the variation in TGW is associated with variation in grain shape, specifically grain thickness and grain width. Genetic analysis indicated that the O. grandiglumis allele for small seed was dominant over the Hwaseong allele. SSR markers tightly linked to the GW QTL would be useful in marker-assisted selection for variation in GW in breeding program.
Genetics and Molecular Research, 2012
A limited backcross procedure was utilized to introgress genes associated with grain quality traits from Oryza rufipogon (Accession No. IRGC 105491), a wild rice from Malaysia, to the cultivated rice O. sativa cv. MR219, a popular high yielding Malaysian rice cultivar. A set of 10 BC 2 F 7 progenies were selected based on the field performance and phenotypic appearance in BC 2 F 5 and BC 2 F 6 generations, which initially started with 266 progenies in the BC 2 F 2 generation. These 10 advanced breeding lines are similar to each other but differ in several important grain quality traits, which can be traced to O. rufipogon introgressions. Phenotyping and genotyping of BC 2 F 7 variants were considered for QTL analysis. The introgressed lines did not show any significant changes compared to the recurrent parent MR219 for the traits grain density and milled rice percentage. All 10 progenies showed significantly higher head rice percentages (70-88%) than the recurrent parent ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 11 (3): 3534-3546 (2012) Introgression segments in advanced breeding lines 3535 MR219. Variants G13 and G15 had higher amylose contents than MR219. All variants were analyzed using polymorphic SSR markers. Of the 34 SSR markers, only 18 showed introgression from O. rufipogon for chromosomes 1, 2, 3, 5, 6, 8, 10, and 11. Graphical genotypes were prepared for each variant, and association between the introgression regions and the traits that increased grain quality was visualized. Based on marker trait association, some of the QTLs are stable across environments and genetic backgrounds and could be used universally.