Spikelets Per Panicle Research Articles

Introgression of OsAP47 by marker-assisted selection enhanced resistance against southern rice black-streaked dwarf virus disease

Southern rice black-streaked dwarf virus disease (SRBSDVD) is the most destructive viral disease in rice. In order to breeding resistant cultivars, Insertion-Deletion (InDel) markers were developed linked to OsAP47, the first isolated major resistance gene against SRBSDVD. Marker-assisted selection (MAS) was conducted to introduce this gene into the commercial variety. A rice line carrying homozygous resistance allele of OsAP47 was selected and named Kanghei No. 201 (KH201). Evaluated by artificial inoculation, KH201 showed significantly higher resistance than the recurrent parent Suxiu No.867 (SX867). And no significant differences were detected for KH201 in the yield-related components, including spikelets per panicle (SPP), ripened grains per panicle (RGPP), 1000-grain weight (TGW) and panicles per square meter (PPSM), leading to stable theoretical yield. The results indicated that introgression of OsAP47 improved rice resistance and can avoid yield losses produced by SRBSDVD. KH201 was demonstrated as a resistance material that could be used in rice breeding.

Yield components affected by rice black-streaked dwarf virus disease in rice cultivars with different resistance levels.

Rice black-streaked dwarf virus disease (RBSDVD) is one of the most destructive rice viral diseases, leading to severe yield losses in rice production. However, little is known about the yield-related components associated with the disease and no resistance cultivars have been successfully used in rice breeding. Seven rice cultivars were analyzed in this study, including six commercial rice varieties and a new line Zhongjian No. 201 (ZJ201) containing the resistance gene OsAP47. Resistance levels of these cultivars were evaluated by artificial inoculation and yield components were collected, including panicle length (PL), spikelets per panicle (SPP), ripened grains per panicle (RGPP), as well as panicles per square meter (PPSM) and 1000-grain weight (TGW). Seed setting rate (SSR) were calculated with the data of SPP and RGPP. The results showed that ZJ201 displayed the highest resistance level and most of the commercial rice cultivars exhibited susceptible to RBSDVD. Yields of all the rice cultivars were significantly declined except ZJ201 and yield losses produced by RBSDVD were mainly due to the reduction of PL, SPP, RGPP, and TGW, suggesting that developments of these traits are associated with RBSDV infection. Resistant rice cultivar could reduce yield losses by maintaining normal development of these traits. Significant correlations were identified between resistance levels and the yield components except SSR and PPSM. The results provided useful clues for understanding the mechanisms of RBSDV invasion and its effect on rice production. ZJ201 was demonstrated as a resistance material that could be used in rice breeding.

A Ghd7-centered regulatory network provides a mechanistic approximation to optimal heterosis in an elite rice hybrid.

Heterosis refers to the superior performance of hybrids over their parents, which is a general phenomenon occurring in diverse organisms. Many commercial hybrids produce high yield without delayed flowering, which we refer to as optimal heterosis and is desired in hybrid breeding. Here, we attempted to illustrate the genomic basis of optimal heterosis by reinvestigating the single-locus quantitative trait loci and digenic interactions of two traits, the number of spikelets per panicle (SP) and heading date (HD), using recombinant inbred lines and 'immortalized F2 s' derived from the elite rice (Oryza sativa) hybrid Shanyou 63. Our analysis revealed a regulatory network that may provide an approximation to the genetic constitution of the optimal heterosis observed in this hybrid. In this network, Ghd7 works as the core element, and three other genes, Ghd7.1, Hd1, and Hd3a/RFT1, also have major roles. The effects of positive dominance by Ghd7 and Ghd7.1 and negative dominance by Hd1 and Hd3a/RFT1 in the hybrid background contribute the major part to the high SP without delaying HD; numerous epistatic interactions, most of which involve Ghd7, also play important roles collectively. The results expand our understanding of the genic interaction networks underlying hybrid rice breeding programs, which may be very useful in future crop genetic improvement.

Effects of nitrogen application rate on the photosynthetic pigment, leaf fluorescence characteristics, and yield of indica hybrid rice and their interrelations

A field experiment employing the rice cultivars Qyou6 and Yixiangyou2115 as materials and different nitrogen application rates was conducted in Huangping County, Guizhou Province in 2019 to determine the effects of nitrogen application rate on photosynthetic pigments, leaf fluorescence characteristics, yield, and their interrelations in indica hybrid rice. The results showed that photosynthetic pigment contents generally increased with increasing nitrogen application rate. As the nitrogen rate increased, the maximal quantum yield of PSII (Fv/Fm), actual quantum yield of PSII (ΦPSII), and relative electron transfer rate at PSII (ETR) first decreased and then increased at the booting stage; Fv/Fm and ΦPSII decreased while ETR first increased and then decreased at the heading stage; nevertheless, Fv/Fm and ΦPSII first decreased and then increased but ETR was just the opposite at the maturity stage. Non-photochemical quenching coefficient (qN) and quantum yield of regulatory energy dissipation at PSII (Y(NPQ)) first increased and then decreased whereas quantum yield of non-regulatory energy dissipation at PSII (Y(NO)) first decreased and then increased at the booting, heading, and maturity stages with increasing nitrogen application rate. Photochemical quenching coefficient (qP) showed an increasing trend as the nitrogen rate increased in the range of 150–300 kg/ha at the heading and maturity stages. Photosynthetic pigments, leaf fluorescence characteristics, and yield and its components were significantly correlated. First, chlorophylls a and b were significantly negatively correlated with Fv/Fm while significantly positively correlated with qP at the heading stage. Secondly, Carotenoids were significantly positively correlated with the effective panicle number (EPN) at the booting stage while significantly negatively correlated with the spikelets per panicle (SPP) at the heading stage. Chlorophyll a and carotenoids were significantly positively correlated with EPN but significantly negatively correlated with spikelet filling (SF) at the maturity stage. In addition, qP was significantly negatively correlated with EPN at the booting stage. At the heading stage, Fv/Fm and Y(NO) were significantly negatively correlated with EPN and SPP, respectively, and Fv/Fm and ΦPSII were significantly positively related to SF. Moreover, qP was extremely significantly positively related to EPN whereas Fv/Fm was extremely significantly negatively correlated with grain yield at the maturity stage. Appropriate nitrogen application rates can enhance photosynthetic pigment contents, improve the photochemical efficiency and proportion of the open part of the reaction center of PSII, and promote the quantum efficiency and self-protection ability of PSII, thereby increasing photosynthetic efficiency and yield. Under the conditions adopted in this experiment, a parabolic relationship was observed between the nitrogen application rate and grain yield. The regression analysis results showed that the best nitrogen application rate of indica hybrid rice is 168.16 kg ha−1 and the highest yield is 11,804.87 kg ha−1.

CARACTERIZACIÓN MORFOLOGICA DE GENOTIPOS DE PASTO BUFFEL CON POTENCIAL PARA PRODUCCIÓN DE FORRAJE Y SEMILLA

El pasto buffel (Pennisetum ciliare L.) es una especie forrajera importante. Es necesario continuar con la exploración de la variabilidad natural de este pasto y seleccionar materiales con potencial para la ganadería. Actualmente el Instituto Internacional de Investigaciones Pecuarias (ILRI, por sus siglas en inglés) en Etiopía conserva de manera ex situ 157 materiales de buffel; es importante caracterizarlos para identificar materiales con potencial productivo. El objetivo del presente estudio fue determinar la diversidad fenotípica de 147 ecotipos y 10 variedades de pasto buffel e identificar materiales con potencial de producción de forraje y semilla. El estudio se realizó en 2014 en la estación experimental Zwai en Etiopía. Los materiales se establecieron en parcelas con 36 plantas cada una. Las variables medidas indirectamente para identificar ecotipos con potencial para la producción de semilla fueron: panículas por planta (PP), espiguillas por panícula (EP) cariópsides por panícula (CP) y días a 50 % de floración (DF), mientras que para producción de forraje las variables fueron altura de planta (AP, cm) y de forraje (AF, cm). Se realizaron análisis de agrupamiento y discriminante. La colección de pasto buffel mostró alta variabilidad en todas las características medidas. Los intervalos de altura de planta y forraje fueron de 34 a 139 y de 24 a 118 cm, respectivamente. La variación de PP fue de 6 a 322, EP de 13 a 285 y para CP fue de 3 a 113. El corte de estandarización al 50 % de floración fue de 48 a 71 días. Se observó una alta correlación (r = 0.98) entre altura de planta y de forraje, y una correlación negativa (r = -0.62) entre panículas por planta y días al 50 % de floración. Cuatro grupos (P < 0.0001) fueron identificados para los 157 materiales. Con excepción de AF, las demás variables contribuyeron significativamente a la separación de grupos. La colección de pasto buffel presentó alta variabilidad en las características medidas; además, los ecotipos 1442, 19448, 19457, 19459, 19462 y 19464 mostraron potencial forrajero.

Genetic Interactions Among Ghd7, Ghd8, OsPRR37 and Hd1 Contribute to Large Variation in Heading Date in Rice

BackgroundHeading date is crucial for rice reproduction and geographic expansion. Many heading date genes are sensitive to photoperiod and jointly regulate flowering time in rice. However, it is not clear how these genes coordinate rice heading.ResultsHere, we performed a genetic interaction analysis among four major rice heading date genes Ghd7, Ghd8, OsPRR37/Ghd7.1 (hereafter PRR37) and Hd1 in the near-isogenic background under both natural long-day (NLD) and natural short-day (NSD) conditions. The 4-gene segregating population exhibited a large heading date variation with more than 95 days under NLD and 42 days under NSD conditions. Tetragenic, trigenic and digenic interactions among these four genes were observed under both conditions but more significant under NLD conditions. In the functional Hd1 backgrounds, the strongest digenic interaction was Ghd7 by Ghd8 under NLD but was Ghd7 by PRR37 under NSD conditions. Interestingly, PRR37 acted as a flowering suppressor under NLD conditions, while it functioned alternatively as an activator or a suppressor under NSD conditions depending on the status of the other three genes. Based on the performances of 16 homozygous four-gene combinations, a positive correlation between heading date and spikelets per panicle (SPP) was found under NSD conditions, but changed to a negative correlation when heading date was over 90 days under NLD conditions.ConclusionsThese results demonstrate the importance of genetic interactions in the rice flowering regulatory network and will help breeders to select favorable combinations to maximize rice yield potential for different ecological areas.

Varietal differences in tiller and panicle development determining the total number of spikelets per unit area in rice

ABSTRACT Rice varietal differences were compared between japonica type (JAT) and indica type (INT) and between panicle number type (PNT) and panicle weight type (PWT) in terms of tiller and panicle development. Rice varieties PNT-JAT Hinohikari, PWT-JAT Akenohoshi, PNT-INT IR36, and PWT-INT Takanari were used in the field experiments. Tiller bud formation and tiller leaf emergence occurred slightly later in the PWT than in the PNT varieties. These parameters occurred slightly earlier in the INT than in the JAT varieties. The maximum number of tillers was greater in IR36 than in Takanari, Hinohikari, and Akenohoshi. The number of panicles per unit area (PN) was greater in IR36 and Hinohikari than in Akenohoshi and Takanari. The widths of the shoot apical meristem (SAM) just before panicle initiation were in the order of Akenohoshi > Hinohikari = Takanari > IR36. The number of spikelets per panicle (SN) was in the order of Takanari = Akenohoshi > IR36 > Hinohikari. In conclusion, the PWT varieties, which had relatively wider SAM, presented with the promotion of main shoot development and the suppression of tiller development. Consequently, PN decreased and SN increased in PWT varieties. INT varieties presented with the promotion of tiller and rachis branch development, which resulted in increases in both PN and SN. These developmental factors may determine varietal differences in the total number of spikelets per unit area. Abbreviations CGR: crop growth rate; DEL: differences between the numbers of emerged leaves in the tiller and those in the main shoot; DIL: differences between the number of initiated leaves in the tiller and those in the main shoot; INT: indica type; JAT: japonica type; MLAI: mean leaf area index; NAR: net assimilation rate; PN: the number of panicles per unit area; SN: the number of spikelets per panicle; PNT: panicle number type; PWT: panicle weight type; SAM: shoot apical meristem; TSN: the total number of spikelets per unit area

Duplication of an upstream silencer of FZP increases grain yield in rice.

Transcriptional silencer and copy number variants (CNVs) are associated with gene expression. However, their roles in generating phenotypes have not been well studied. Here we identified a rice quantitative trait locus, SGDP7 (Small Grain and Dense Panicle 7). SGDP7 is identical to FZP (FRIZZY PANICLE), which represses the formation of axillary meristems. The causal mutation of SGDP7 is an 18-bp fragment, named CNV-18bp, which was inserted ~5.3 kb upstream of FZP and resulted in a tandem duplication in the cultivar Chuan 7. The CNV-18bp duplication repressed FZP expression, prolonged the panicle branching period and increased grain yield by more than 15% through substantially increasing the number of spikelets per panicle (SPP) and slightly decreasing the 1,000-grain weight (TGW). The transcription repressor OsBZR1 binds the CGTG motifs in CNV-18bp and thereby represses FZP expression, indicating that CNV-18bp is the upstream silencer of FZP. These findings showed that the silencer CNVs coordinate a trade-off between SPP and TGW by fine-tuning FZP expression, and balancing the trade-off could enhance yield potential.

Genome‐Wide Association Analysis Reveals Different Genetic Control in Panicle Architecture Between Indica and Japonica Rice

Panicle architecture determines the number of spikelets per panicle (SPP) and is highly associated with grain yield in rice ( L.). Understanding the genetic basis of panicle architecture is important for improving the yield of rice grain. In this study, we dissected panicle architecture traits into eight components, which were phenotyped from a germplasm collection of 529 cultivars. Multiple regression analysis revealed that the number of secondary branch (NSB) was the major factor that contributed to SPP. Genome-wide association analysis was performed independently for the eight particle architecture traits observed in the and rice subpopulations compared with the whole rice population. In total, 30 loci were associated with these traits. Of these, 13 loci were closely linked to known panicle architecture genes, and 17 novel loci were repeatedly identified in different environments. An association signal cluster was identified for NSB and number of spikelets per secondary branch (NSSB) in the region of 31.6 to 31.7 Mb on chromosome 4. In addition to the common associations detected in both and subpopulations, many associated loci were unique to one subpopulation. For example, and were specifically associated with panicle length (PL) in and rice, respectively. Moreover, the -mediated flowering genes and were associated with the formation of panicle architecture in rice. These results suggest that different gene networks regulate panicle architecture in and rice.

Detection of additive and additive×environment interaction effects of QTLs for yield‐component traits of rice using single‐segment substitution lines (SSSLs)

AbstractAdditive effects (A) and additive‐by‐environment interactions (A×E) for five rice yield components were analysed using 20 SSSLs under mixed linear model methodology. Thirty‐one QTLs were detected. Different yield components have different QTL‐by‐environment (Q×E) interaction patterns. No A×E interaction effects were detected for the four QTLs for panicle number (PN). Four QTLs detected for spikelets per panicle (SPP) had A×E interactions. Five of seven QTLs detected for grains per panicle (GPP), two of 10 QTLs detected for 1000‐grains weight (GWT) and three of six QTLs detected for seed set ratio (SSR) showed significant A×E interaction. Most of these QTLs were distributed in clusters across the genome. The complexity of linkage and pleiotropy of these QTLs plus environmental effect may result in the diversity of the yield phenotype in the SSSLs. Only S19 exhibited a significant increase in yield with a predicted gain by 281.58 kg ha−1. The results may be useful to design a better breeding strategy that takes advantage of QTL‐by‐environment interaction effects in each of the SSSLs.

High-density mapping of quantitative trait loci for grain-weight and spikelet number in rice.

BackgroundHigh grain yield is one of the most important traits requiring improvement in rice breeding programs. Consequently, the genetic basis of spikelets per panicle (SPP) and grain weight (TGW) have received much research focus because of their importance in rice yield.ResultsIn this study, IL28, which is a near isogenic line (NIL) developed by introgressing chromosomal segments of the cultivar ‘Moroberekan’ into the cultivar ‘Ilpumbyeo’, showed a significant increase in the number of spikelets per panicle (SPP) and 1,000-grain weight (TGW) compared to the recurrent parent, Ilpumbyeo. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo indicated that both qSPP6 and qTGW6 are located in the interval RM3430–RM20580. Following substitution mapping with 50 F3:4:5 lines, qSPP6 was mapped to a 429-kb interval between RM20521 and InDel-1, while qTGW6 was mapped to a 37.85-kb interval between InDel-1 and SNP--3 based on the japonica genome sequence. This result indicates that qSPP6 and qTGW6 are different genes. Yield trials with substitution lines indicated that lines harboring the homozygous Moroberekan segment at both the qSPP6 and qTGW6 region showed significantly higher grain yield than Ilpumbyeo.ConclusionBecause the Moroberekan alleles for SPP and TGW have been shown to be beneficial in the genetic background of Ilpumbyeo, both the qSPP6 and qTGW6 alleles might prove valuable in improving rice yields. Closely linked SSR markers are expected to facilitate the cloning of genes that underlie these QTLs, as well as with marker-assisted selection for variation in SPP and TGW in rice breeding programs.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-014-0014-5) contains supplementary material, which is available to authorized users.

Validation of QTLs associated with spikelets per panicle and grain weight in rice

In this study, a near-isogenic line (BC4F10) CR572 developed by introgressing a chromosomal segment fromOryza rufipogon(accession no. 105491) into theOryza sativasubsp.japonicacv. Hwaseong was found to exhibit a significant increase in the number of spikelets per panicle (SPP) and grain weight compared with the recurrent parent Hwaseong. Quantitative trait locus (QTL) analysis in F2generation derived from the cross between CR572 and Hwaseong revealed that two QTLs,qSPP1andqTGW1, were linked to a simple sequence repeat marker, RM283, on chromosome 1. The additive effect of theO. rufipogonallele atqSPP1was 13 SPP, and 21.6% of the phenotypic variance was explained by the segregation of RM283. TheqTGW1QTL explained 19.1% of the phenotypic variance for grain weight. Substitution mapping was carried out with five F3lines derived from F2plants having informative recombination breakpoints within the target region. Substitution mapping indicated the linkage ofqSPP1andqTGW1. The grain yield of CR572 was 18.2 and 15.8% higher than that of Hwaseong at two locations, respectively, mainly due to the increase in 1000-grain weight and SPP. These results are very useful for QTL cluster transfer by molecular marker-assisted selection in rice breeding programmes and for QTL gene cloning by map-based cloning.

QTL Analysis of Yield Components in Rice Using a Cheongcheong/Nagdong Doubled Haploid Genetic Map

In this study, only two of 12 quantitative trait loci (QTLs) affecting yield and yield components were identified in a single year, indicating that individual QTLs are probably sensitive to the environment. A rice growth survey of “Cheongcheong” and “Nag dong” in a doubled haploid population in 2012 revealed that yield capacity was influenced by climate change. Analysis of yield and yield components indicated that five average traits are high in “Cheongcheong”. Frequency distribution tables indicated that panicles per plant (PPP), spike lets per panicle (SPP), and 1000-grain weight (TGW) were normally distributed. The strongest relationship was identified between SPP and seed set percentage (SSP) among phenotypic correlations related to yield and yield components found on chromosomes 2, 3, 6, 8 in 2012. SPP and SSP was a very relevant requisite about quantity. Analysis of QTL about quantity was total 9. In the present study, a doubled haploid population was used to analyze the epistatic effects on yield and yield components in rice. Although other epistatic QTLs were not included in any of the main-effect QTLs, they significantly influenced the traits. These results indicated that epistatic interaction plays an important role in controlling the expression of complex traits. Thus, the utilization of marker-assisted selection in rice breeding programs should take epistatic effects into consideration. Hence, the QTLs responsible for major effects are more suitable for marker-assisted selection programs to improve yield and related traits across different environments.

Analysis of High-Resolution QTL Markers Associated with Rice Yields Using Data for Two Consecutive Years in Different Environmental Conditions

Previously we reported the identification of seven quantitative trait loci (QTLs) associated with the rice yield measuring five parameters including panicles per plant (PPP), spikelets per panicle (SPP), seed set percentage (SSP), 1000-grain weight (TGW) and yield in 2012. Here we report the analysis of QTLs using the same trait parameters data of the mapping population in 2013 for detecting highly conserved QTL markers. A total of 6 QTLs were identified from chromosomes 1, 7, 8, 10, 11, and 12, which were contrasted with our previous results (chromosomes 1, 2, 4, 5, 6, 8, and 11). In this comparison, three QTLs from chromosome 1, 8, and 11 were only found to be associated with the components of yield over two consecutive years indicating high sensitivity of QTL markers to the environment. Of those three QTLs, SPP-associated marker RM12285 was found to be dominantly expressed by real-time PCR (qPCR). In addition, compared to our previous report the numbers of mapping population and markers were significantly increased for higher resolution markers from 70 to 120, and from 143 to 217, respectively. We also found that the parameter SPP was dominantly correlated with the rice yield. Furthermore, the double haploid (DH) population facilitated to analyze the epistatic effects for yield and yield components in rice. Taken together, combining multiple mapping population data over years possibly enables narrowing down to the highly conserved QTL markers against diverse environmental fluctuation caused by such as drought and high temperature. Thus, these data would be critically exploited to improve for the crop breeding strategy.

QTL mapping reveals a tight linkage between QTLs for grain weight and panicle spikelet number in rice

BackgroundA number of QTL studies reported that one genomic region was associated with several traits, indicating linkage and/or pleiotropic effects. The question of pleiotropy versus tight linkage in these studies should be solved using a large-size population combined with high-density mapping. For example, if each of the 2 parents has a TGW-increasing or SPP-increasing QTL that is tightly linked, complementary combination of the 2 beneficial QTLs by using molecular markers could produce higher yields compared to the 2 parents. However, a pleiotropic QTL with opposite effects on the SPP and 1,000-grain weight (TGW) is complicated and challenging in terms of its application to rice improvement.ResultsIn this study, using a series of BC5F4 nearly isogenic lines (NILs) that were derived from a cross between the Korean japonica cultivar Hwayeongbyeo and Oryza rufipogon, we demonstrated that 2 QTLs, qSPP5 for spikelets per panicle (SPP) and qTGW5 for grain weight (TGW), are tightly linked on chromosome 5. Alleles from the O. rufipogon parent increased the SPP and decreased TGW in the Hwayeongbyeo background. qSPP5 was located within a 803-kb interval between the simple sequence repeat (SSR) markers INDEL3 and RM18076. Based on the map position, qTGW 5 seemed to be the same gene as qSW5, which controls grain morphology. The additive effect of the O. rufipogon allele at qSPP5 was 10–15 SPP, and 33.0% of the phenotypic variance could be explained by the segregation of the SSR marker RM18058. Yield trials with BC5F4 NILs showed that lines that contained a homozygous O. rufipogon introgression at the qSPP5 region out-yielded sibling NILs that contained Hwayeongbyeo DNA by 15.3% and out-yielded the Hwayeongbyeo parent by 7.3%.ConclusionBased on the finding that the O. rufipogon allele for the SPP was beneficial in the japonica and indica cultivar backgrounds, the qSPP5 allele could be valuable for improving rice yields. In addition, the NIL populations and molecular markers are useful for cloning qSPP5.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-6-33) contains supplementary material, which is available to authorized users.

Validation and Characterization of Ghd7.1, a Major Quantitative Trait Locus with Pleiotropic Effects on Spikelets per Panicle, Plant Height, and Heading Date in Rice (Oryza sativa L.)

A quantitative trait locus (QTL) that affects heading date (HD) and the number of spikelets per panicle (SPP) was previously identified in a small region on chromosome 7 in rice (Oryza sativa L.). In order to further characterize the QTL region, near isogenic lines (NILs) were quickly obtained by self-crossing recombinant inbred line 189, which is heterozygous in the vicinity of the target region. The pleiotropic effects of QTL Ghd7.1 on plant height (PH), SPP, and HD, were validated using an NIL-F2 population. Ghd7.1 explained 50.2%, 45.3%, and 76.9% of phenotypic variation in PH, SPP, and HD, respectively. Ghd7.1 was precisely mapped to a 357-kb region on the basis of analysis of the progeny of the NIL-F2 population. Day-length treatment confirmed that Ghd7.1 is sensitive to photoperiod, with long days delaying heading up to 12.5 d. Identification of panicle initiation and development for the pair of NILs showed that Ghd7.1 elongated the photoperiod-sensitive phase more than 10 d, but did not change the basic vegetative phase and the reproductive growth phase. These findings indicated that Ghd7.1 regulates SPP by controlling the rate of panicle differentiation rather than the duration of panicle development.

Identification and validation of a yield-enhancing QTL cluster in rice (Oryza sativa L.)

Improvement of rice grain yield (YD) is an important goal in rice breeding. YD is determined by its related traits such as spikelet fertility (SF), 1,000-grain weight (TGW), and the number of spikelets per panicle (SPP). We previously mapped quantitative trait loci (QTLs) for SPP and TGW using the recombinant inbred lines (RILs) derived from the crosses between Minghui 63 and Teqing. In this study, four QTLs for SF and four QTLs for YD were detected in the RILs. Comparison of the locations of QTLs for these three yield-related traits identified one QTL cluster in the interval between RM3400 and RM3646 on chromosome 3. The QTL cluster contained three QTLs, SPP3a, SF3 and TGW3a, but no YD QTL was located there. To validate the QTL cluster, a BC4F2 population was obtained, in which SPP3a, SF3 and TGW3a were simultaneously mapped to the same region. SPP3a, SF3 and TGW3a explained 36.3, 29.5 and 59.0 % of phenotype variance with additive effect of 16.4 spikelets, 6 % SF and 1.8 g grain weight, respectively. In the BC4F2 population, though the region has opposite effects on TGW and SPP/SF, a YD QTL YD3 identified in this cluster region can increase 4.6 g grains per plant, which suggests this QTL cluster is a yield-enhancing QTL cluster and can be targeted to improve rice yield by marker aided selection.

Fine Mapping of a Quantitative Trait Loci Controlling the Number of Spikelets per Panicle in Rice

Spikelets per panicle (SPP) is one of the most important traits associated with rice yield. In this study, IL28, a near isogenic line (NIL) developed by introgressing chromosomal segments from ‘Moroberekan’ into ‘Ilpumbyeo’ showed significantly higher number of spikelets per panicle than the recurrent parent, ‘Ilpumbyeo’. Quantitative trait locus (QTL) analysis in 243 F2 plants derived from a cross between IL28 and Ilpumbyeo indicated that a QTL for spikelets per panicle, qSPP6 was located in the interval RM3430 - RM20580. The Moroberekan allele increased SPP. The fact that QTLs for panicle length and the number of secondary branches were mapped in the same interval as qSPP6 appears to indicate that this locus was associated with panicle structure. To map the QTL more precisely, substitution mapping of qSPP6 using F3 lines was conducted. Substitution mapping with 41 F3 lines further narrowed the interval containing not only qSPP6 for spikelets per panicle but also qNDW6 for node width to about 680-kb between markers RM20521 and RM20572 based on Nipponbare genome sequence. The locus, qSPP6 is of particular interest because of its independence from undesirable height and flowering time. SSR markers tightly linked to the qSPP6 will facilitate cloning of the gene underlying this QTL as well as marker assisted selection for variation in SPP in the breeding program.

Fine mapping of a QTL for the number of spikelets per panicle by using near‐isogenic lines derived from an interspecific cross between Oryza sativa and Oryza minuta

AbstractWe constructed a high‐resolution physical map for the qSPP7 QTL for spikelets per panicle (SPP) on rice chromosome 7 across a 28.6‐kb region containing four predicted genes. Using a series of BC7F4 near‐isogenic lines (NILs) derived from a cross between the Korean japonica cultivar ‘Hwaseongbyeo’ and Oryza minuta (IRGC Acc. No. 101144), three QTLs for the number of SPP, grains per panicle and primary branches were identified in the cluster (P ≤ 0.01). All three QTLs were additive, and alleles from the O. minuta parent were beneficial in the ‘Hwaseongbyeo’ background. qSPP7 was mapped to a 28.6‐kb region between the two simple sequence repeat (SSR) markers RM4952 and RM21605. The additive effect of the O. minuta allele at qSPP7 was 23 SPP, and 43.6% of the phenotypic variance was explained by the segregation of the SSR marker RM4952. Colocalization of the three QTLs suggested that this locus was associated with panicle structure and had pleiotropic effects. The NIL populations and molecular markers are useful for cloning qspp7.

Identification of Quantitative Trait Loci for Bacterial Blight Resistance Derived from Oryza meyeriana and Agronomic Traits in Recombinant Inbred Lines of Oryza sativa

AbstractBacterial blight (BB) is one of the major diseases that affect rice productivity. In previous studies, BB resistance was transferred to cultivated rice Oryza sativa from wild rice Oryza meyeriana using asymmetric somatic hybridization. One of the resistant hybrid progenies (Y73) has also been shown to possess novel resistance gene(s) different from any of those previously associated with BB resistance. We have mapped quantitative trait loci (QTLs) for BB resistance in a recombinant inbred line (RIL) population derived from a cross between Y73 and a BB‐susceptible cv. IR24. Five QTLs were detected where Y73 alleles contributed to increased BB resistance. Three minor QTLs were identified on chromosomes 3, 10 and 11, and two major QTLs on chromosomes 1 and 5, respectively. QTL on chromosome 5, designated qBBR5, had the strongest effect on BB resistance, explaining approximately 37% of the phenotypic variance. Using the same RIL population, we also mapped QTLs for agronomic traits including plant height (PH), heading date (HD), plant yield (PYD) and PYD component traits. A total of 21 QTLs were identified, of which four were detected for PH, six for HD, three for panicle number per plant (PNPP), one for spikelets per panicle (SPP), six for 1000‐grain weight (TGW) and one for PYD. qPH1 (a QTL for PH) was found in the same interval as qBBR1 for BB resistance, and qHD11 for HD and qBBR11 for BB resistance also shared a similar interval. Additionally, BB resistance was significantly correlated with PH or HD in the RIL population. This suggests that the resistance genes may have pleiotropic effects on, or close linkage to, genes controlling PH or HD. These results will help deduce the resistance mechanisms of the novel resistance gene(s) and provide the basis for cloning them and using them in marker‐assisted breeding.