Single Segment Substitution Lines Research Articles

The protective roles of Oryza glumaepatula and phytohormone in enhancing rice tolerance to cadmium stress by regulating gene expression, morphological, physiological, and antioxidant defense system.

The heavy metal cadmium (Cd) is highly poisonous and has received significant attention from environmental scientists due to its harmful impacts on plants. Oryza glumaepatula is a wild rice that contains useful genes against biotic and abiotic stresses. Therefore, the current study used SG007, a single-segment substitution line (SSSL), generated by crossing O. glumaepatula with an elite rice cultivar (HJX74), to evaluate the resistance potential against Cd. Moreover, we assessed the efficacy of strigolactone GR24 (1 μM) against Cd toxicity (100 μM) by investigating physiological, biochemical, and molecular mechanisms in both cultivars (i.e., SG007 and HJX74). The findings of this study revealed that Cd toxicity declined the chlorophyll a, chlorophyll b, and carotenoids by 50%, 20%, and 44% in SG007, and 58%, 39%, and 59% in HJX74 by enhancing electrolyte leakage (EL), malondialdehyde (MDA), and hydrogen peroxide (H2O2) by 113%, 184%, and 119% in SG007 and 248%, 273% and 195% in HJX74, respectively. GR24 improved growth under Cd stress in both cultivars, and SG007 exhibited better plant growth parameters, antioxidant enzymatic activities, nitric oxide synthase (NOS), and nitric oxide (NO) levels than HJX74 under Cd toxicity. GR24 with SG007 regulated expressions of Cd transporters and reduced the cytological disruptions in cell organelles. The combined utilization of SG007 and GR24 reduced Cd accumulation and oxidative stress and improved plant growth parameters and enzymatic activities. In conclusion, our study highlights the potential of utilizing SG007 in conjunction with GR24 as a practical strategy to mitigate Cd pollution in rice. The results not only underscore the beneficial effects of strigolactone GR24 in alleviating Cd-induced stress but also emphasize the valuable genetic traits of O. glumaepatula in developing rice lines with enhanced tolerance to heavy metals, offering broader implications for sustainable agriculture and crop improvement in contaminated environments.

Natural variation in the promoter of qRBG1/OsBZR5 underlies enhanced rice yield

Seed size, a key determinant of rice yield, is regulated by brassinosteroid (BR); however, the BR pathway in rice has not been fully elucidated. Here, we report the cloning and characterization of the quantitative trait locus Rice Big Grain 1 (qRBG1) from single-segment substitution line Z499. Our data show that qRBG1Z is an unselected rare promoter variation that reduces qRBG1 expression to increase cell number and size, resulting in larger grains, whereas qRBG1 overexpression causes smaller grains in recipient Nipponbare. We demonstrate that qRBG1 encodes a non-canonical BES1 (Bri1-EMS-Suppressor1)/BZR1(Brassinazole-Resistant1) family member, OsBZR5, that regulates grain size upon phosphorylation by OsGSK2 (GSK3-like Kinase2) and binding to D2 (DWARF2) and OFP1 (Ovate-Family-Protein1) promoters. qRBG1 interacts with OsBZR1 to synergistically repress D2, and to antagonistically mediate OFP1 for grain size. Our results reveal a regulatory network controlling grain size via OsGSK2–qRBG1–OsBZR1–D2–OFP1 module, providing a target for improving rice yield.

Oryza glumaepatula and calcium oxide nanoparticles enhanced Cr stress tolerance by maintaining antioxidant defense, chlorophyll and gene expression levels in rice

Chromium (Cr), a potent heavy metal, threatens rice cultivation due to its escalating presence in soil from human activities. Wild rice contains useful genes for phytoremediation; however, it is difficult to use directly for metal mitigation. Here, a single segment substitution line (SSSL), SG001, was developed by crossing O. glumaepatula and Huajingxian74 (HJX) to evaluate the survival ability of plants against Cr. Further, we explored the potential effect of calcium oxide nanoparticles (CaO-NPs) (50 μM) to minimize the toxic effect of Cr (100 μM) in rice cultivars, SG001 and HJX. The findings of this study indicated that Cr toxicity led to increased oxidative stress. This was shown by higher levels of hydrogen peroxide (H2O2), which was increased by 104% in SG001 and 177% in HJX, and malondialdehyde (MDA) increased by 79% in SG001 and 135% in HJX. Furthermore, it also depicted that Cr toxicity considerably declined shoot and root length, shoot and root fresh weight by 30%, 27%, 25%, and 20% in SG001 and 44%, 51%, 42%, and 45% in HJX, respectively. This mitigation was evidenced by decreased Cr contents, increased calcium (Ca) levels in SG001, and the maintenance of chlorophyll, antioxidant defense, and gene expression levels. Moreover, there was a notable reduction in MDA and H2O2, while the defense mechanisms of key antioxidants, including ascorbate peroxidase, superoxide dismutase, glutathione, catalase, and peroxidase were upregulated, along with an increase in soluble protein contents in both rice cultivars after applying CaO-NPs. CaO-NPs effectively restored cellular and subcellular structural integrity and growth in both lines, which had been seriously disrupted by Cr toxicity. Overall, our findings suggest that SG001, in combination with CaO-NPs, could serve as an effective strategy to mitigate Cr toxicity in plants.

Design of rice with low cadmium accumulation in grain using single segment substitution line

Rice (Oryza sativa L.) is a major dietary source of cadmium (Cd). Developing rice varieties with reduced Cd levels in the grain is a cost-effective and practical approach to enhance food safety, particularly in regions with high Cd contamination. However, the genetic mechanisms underlying Cd accumulation in rice grains are not fully understood. In this study, we identified eight quantitative trait loci (QTLs) associated with Cd accumulation in rice grains through substitution mapping using single segment substitution lines (SSSLs). These QTLs, named qCd‐2‐1, qCd‐3‐1, qCd‐3‐2, qCd‐5‐1, qCd‐6‐1, qCd‐7‐1, qCd‐8‐1, and qCd‐11‐1, are distributed across seven chromosomes. Notably, the qCd‐5‐1 and qCd‐6‐1 loci are reported for the first time. We performed a detailed haplotype analysis of candidate genes related to heavy metal metabolism, specifically focusing on Cd accumulation. All SSSLs carrying alleles from donor parents exhibited a significant reduction in Cd accumulation, with additive effects ranging from −0.061 to −0.105. To further develop rice varieties with lower Cd accumulation in the grain, we developed six pyramided lines through crossing and marker-assisted selection. These pyramided lines showed significantly reduced Cd content in the grain compared to the elite indica recurrent parent, Huajingxian74 (HJX74). Importantly, most agronomic characteristics of the pyramided lines were similar to those of HJX74. In conclusion, this study demonstrates that identifying and pyramiding QTLs associated with reduced Cd accumulation is an effective strategy for developing rice varieties with lower Cd content in the grain.

Fine mapping and candidate gene analysis of qSRC3 controlling the silk color in maize (Zea mays L.).

Fine mapping of the maize QTL qSRC3, responsible for red silk, uncovered the candidate gene ZmMYB20, which encodes an R2R3-MYB transcription factor, has light-sensitive expression, and putatively regulates genes expression associated with anthocyanin biosynthesis. Colorless silk is a key characteristic contributing to the visual quality of fresh corn intended for market distribution. Nonetheless, the identification of Mendelian trait loci and associated genes that control silk color has been scarce. In this study, a F2 population arising from the hybridization of the single-segment substitution line qSRC3MT1 with red silk, carrying an introgressed allele from teosinte (Zea mays ssp. mexicana), and the recurrent maize inbred line Mo17, characterized by light green silk, was utilized for fine mapping. We found that the red silk trait is controlled by a semi-dominant genetic locus known as qSRC3, and its expression is susceptible to light-mediated inhibition. Moreover, qSRC3 explained 68.78% of the phenotypic variance and was delimited to a 133.2kb region, which includes three genes. Subsequent expression analyses revealed that ZmMYB20 (Zm00001d039700), which encodes an R2R3-MYB transcription factor, was the key candidate gene within qSRC3. Yeast one-hybrid and dual-luciferase reporter assays provided evidence that ZmMYB20 suppresses the expression of two crucial anthocyanin biosynthesis genes, namely ZmF3H and ZmUFGT, by directly binding to their respective promoter regions. Our findings underscore the significance of light-inhibited ZmMYB20 in orchestrating the spatial and temporal regulation of anthocyanin biosynthesis. These results advance the production of colorless silk in fresh corn, responding to the misconception that fresh corn with withered colored silk is not fresh and providing valuable genetic resources for the improvement of sweet and waxy maize.

Fine-Mapping and Candidate Gene Analysis of qSERg-1b from O. glumaepatula to Improve Stigma Exsertion Rate in Rice

The stigma exsertion rate (SER) is one of the important factors affecting the seed production of hybrid rice. In the genus Oryza, wild rice species usually show higher SERs than cultivars. We previously identified one novel SER-QTL, qSERg-1b, from the single-segment substitution line (SSSL) SG22 of O. glumaepatula. In this study, qSERg-1b was fine-mapped by developing the secondary SSSLs (s-SSSLs) of SG22 and substitution mapping among the s-SSSLs. A total of 11 s-SSSLs were developed and used for qSERg-1b fine-mapping. As a result, qSERg-1b was narrowed down to the 122.59 kb physical region between InDel markers M01 and M49. There were 19 genes annotated in both O. glumaepatula and the HJX74 genomes at the qSERg-1b interval. Based on the genome re-sequencing of SG22 and HJX74, and the expression levels of the annotated functional genes, multiple nucleotide variations were found in LOC_Os01g53630, LOC_Os01g53680, and LOC_Os01g53710, including base substitutions and insertions/deletions of the genes, and they also showed significant differences in expression levels between SG22 and HJX74. Therefore, LOC_Os01g53630, LOC_Os01g53680, and LOC_Os01g53710 were selected as the most possible candidate genes of qSERg-1b for further validation. The above results laid an important foundation for qSERg-1b cloning and provided valuable resources for molecular breeding of SER in rice.

Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness

Rice chalkiness is a key limiting factor of high-quality rice. The breeding of low chalkiness varieties has always been a challenging task due to the complexity of chalkiness and its susceptibility to environmental factors. In previous studies, we identified six QTLs for the percentage of grain chalkiness (PGC), named qPGC5, qPGC6, qPGC8.1, qPGC8.2, qPGC9 and qPGC11, using single-segment substitution lines (SSSLs) with genetic background of Huajingxian 74 (HJX74). In this study, we utilized the six low chalkiness QTLs to develop 17 pyramiding lines with 2–4 QTLs. The results showed that the PGC decreased with the increase of QTLs in the pyramiding lines. The pyramiding lines with 4 QTLs significantly reduced the chalkiness of rice and reached the best quality level. Among the six QTLs, qPGC5 and qPGC6 showed greater additive effects and were classified as Group A, while the other four QTLs showed smaller additive effects and were classified as Group B. In pyramiding lines, although the presence of epistasis, additivity remained the main component of QTL effects. qPGC5 and qPGC6 showed stronger ability to reduce rice chalkiness, particularly in the environment of high temperature (HT) in the first cropping season (FCS). Our research demonstrates that by pyramiding low chalkiness QTLs, it is feasible to develop the high-quality rice varieties with low chalkiness at the best quality level even in the HT environment of FCS.

QTL epistasis plays a role of homeostasis on heading date in rice

If there was no gene interaction, the gene aggregation effect would increase infinitely with the increase of gene number. Epistasis avoids the endless accumulation of gene effects, playing a role of homeostasis. To confirm the role, QTL epistases were analyzed by four single-segment substitution lines with heading date QTLs in this paper. We found that QTLs of three positive effects and one negative effect generated 62.5% negative dual QTL epistatic effects and 57.7% positive triple QTL epistatic effects, forming the relationship “positive QTLs-negative one order interactions-positive two order interactions”. In this way, the aggregation effect of QTLs was partially neutralized by the opposite epistatic effect sum. There also were two exceptions, QTL OsMADS50 and gene Hd3a-2 were always with consistent effect directions with their epistases, implying they could be employed in pyramiding breeding with different objectives. This study elucidated the mechanism of epistatic interactions among four QTLs and provided valuable genetic resources for improving heading date in rice.

Development of Single-Segment Substitution Lines and Fine-Mapping of qSPP4 for Spikelets Per Panicle and qGW9 for Grain Width Based on Rice Dual-Segment Substitution Line Z783.

Single segment substitution line (SSSL) libraries are an ideal platform for breeding by design. To develop SSSLs-Xihui18 covering the whole genome, a novel rice chromosome segment substitution line (CSSL), Z783, carrying two substitution segments (average length of 6.55 Mb) on Chr.4 and Chr.9 was identified, which was a gap in the library previously. Z783 was developed from the progeny of recipient "Xihui18" (an indica restorer line) and donor "Huhan3" (a japonica cultivar) by advanced backcross combined molecular marker-assisted selection (MAS). It displayed multiple panicles and less spikelets and wide grains. Then, a F2 population derived from Xihui18/Z783 was used to map quantitative trait loci (QTLs) for yield-related traits by the mixed linear model method. Nine QTLs were detected (p < 0.05). Furthermore, three SSSLs were constructed by MAS, and all 9 QTLs could be validated, and 15 novel QTLs could be detected by these SSSLs by a one-way ANOVA analysis. The genetic analysis showed that qSSP4 for less spikelets and qGW9 for wide grain all displayed dominant gene action in their SSSLs. Finally, qSSP4 and qGW9 were fine-mapped to intervals of 2.75 Mb and 1.84 Mb, on Chromosomes 4 and 9, respectively. The results lay a solid foundation for their map cloning and molecular breeding by design.

QGLF5 from Oryza rufipogon Griff. improves kernel shape, plant architecture, and yield in rice.

A novel QTL qGLF5 from Oryza rufipogon Griff. improves yield per plant and plant architecture in rice. Kernel size and plant architecture are critical agronomic traits that are key targets for improving crop yield. From the single-segment substitution lines of Oryza rufipogon Griff. in the indica cultivar Huajingxian74 (HJX74) background, we identified a novel quantitative trait locus (QTL), named qGLF5, which improves kernel shape, plant architecture, and yield per plant in rice. Compared with the control HJX74, the plant height, panicles per plant, panicle length, primary branches per panicle, secondary branches per panicle, and kernels per plant of the near-isogenic line-qGLF5 (NIL-qGLF5) are significantly increased. NIL-qGLF5 has long and narrow kernels by regulating cell number, cell length and width in the spikelet hulls. Yield per plant of NIL-qGLF5 is increased by 35.02% compared with that of HJX74. In addition, qGLF5 significantly improves yield per plant and plant architecture of NIL-gw5 and NIL-GW7. These results indicate that qGLF5 might be beneficial for improving plant architecture and kernel yield in rice breeding by molecular design.

The Resistance of Maize to Ustilago maydis Infection Is Correlated with the Degree of Methyl Esterification of Pectin in the Cell Wall.

Common smut caused by Ustilago maydis is one of the dominant fungal diseases in plants. The resistance mechanism to U. maydis infection involving alterations in the cell wall is poorly studied. In this study, the resistant single segment substitution line (SSSL) R445 and its susceptible recurrent parent line Ye478 of maize were infected with U. maydis, and the changes in cell wall components and structure were studied at 0, 2, 4, 8, and 12 days postinfection. In R445 and Ye478, the contents of cellulose, hemicellulose, pectin, and lignin increased by varying degrees, and pectin methylesterase (PME) activity increased. The changes in hemicellulose and pectin in the cell wall after U. maydis infection were analyzed via immunolabeling using monoclonal antibodies against hemicellulsic xylans and high/low-methylated pectin. U. maydis infection altered methyl esterification of pectin, and the degree of methyl esterification was correlated with the resistance of maize to U. maydis. Furthermore, the relationship between methyl esterification of pectin and host resistance was validated using 15 maize inbred lines with different resistance levels. The results revealed that cell wall components, particularly pectin, were important factors affecting the colonization and propagation of U. maydis in maize, and methyl esterification of pectin played a role in the resistance of maize to U. maydis infection.

QGL3.4 controls kernel size and plant architecture in rice.

Kernel size and plant architecture play important roles in kernel yield in rice. Cloning and functional study of genes related to kernel size and plant architecture are of great significance for breeding high-yield rice. Using the single-segment substitution lines which developed with Oryza barthii as a donor parent and an elite indica cultivar Huajingxian74 (HJX74) as a recipient parent, we identified a novel QTL (quantitative trait locus), named qGL3.4, which controls kernel size and plant architecture. Compared with HJX74, the kernel length, kernel width, 1000-kernel weight, panicle length, kernels per plant, primary branches, yield per plant, and plant height of near isogenic line-qGL3.4 (NIL-qGL3.4) are increased, whereas the panicles per plant and secondary branches per panicle of NIL-qGL3.4 are comparable to those of HJX74. qGL3.4 was narrowed to a 239.18 kb interval on chromosome 3. Cell analysis showed that NIL-qGL3.4 controlled kernel size by regulating cell growth. qGL3.4 controls kernel size at least in part through regulating the transcription levels of EXPANSINS, GS3, GL3.1, PGL1, GL7, OsSPL13 and GS5. These results indicate that qGL3.4 might be beneficial for improving kernel yield and plant architecture in rice breeding.

Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara

BackgroundDomestication from wild rice species to cultivated rice is a key milestone, which involved changes of many specific traits and the variations of the genetic systems. Among the AA-genome wild rice species, O. rufipogon and O. nivara, have many favorable genes and thought to be progenitors of O. sativa.ResultsIn the present study, by using O. rufipogon and O. nivara as donors, the single segment substitution lines (SSSLs) have been developed in the background of the elite indica cultivar, HJX74. In the SSSLs population, 11 genes for 5 domestication traits, including tiller angle, spreading panicle, awn, seed shattering, and red pericarp, were identified and mapped on 5 chromosomes through substitution mapping. Herein, allelic variations of 7 genes were found through sequence alignment with the known genes, that is, TA7-RUF was allelic to PROG1, TA8-RUF was allelic to TIG1, SPR4-NIV was allelic to OsLG1, AN4-RUF was allelic to An-1, SH4-NIV was allelic to SH4, and both RC7-RUF and RC7-NIV were allelic to Rc. Meanwhile, 4 genes, TA11-NIV, SPR3-NIV, AN3-NIV, and AN4-NIV, were considered as the novel genes identified in these SSSLs, because of none known genes for the related domestication traits found in the chromosomal locations of them.ConclusionThe results indicated that the SSSLs would be precious germplasm resources for gene mining and utilization from wild rice species, and it laid the foundation for further analyses of the novel domestication genes to better understand the genetic basis in regulating the traits variation during domestication.

Relationships between starch molecular components and eating and cooking qualities of rice using single-segment substitution lines with different Wx loci

Waxy (Wx) gene in rice endosperm synthesizes amylose and amylopectin extra-long chain (ELC). Five rice lines with different Wx locus single-segment substitutions under the same genetic background were investigated for relationships of their starch molecular components and eating and cooking qualities (ECQs) including pasting, thermal, textural and sensory properties. Rice lines with different Wx loci exhibited different ECQs, and their starches had different apparent amylose contents (AACs), true amylose contents (TACs), ELC contents (ELCCs), and amylopectin chain length distributions. The AAC was correlated positively to hardness and cohesiveness of cooked rice, and negatively to adhesiveness and palatability of cooked rice and breakdown viscosity of rice flour. The TAC was correlated positively to gelatinization temperature range and negatively to gelatinization temperature and enthalpy. ELCC showed a positive relationship with pasting peak time of rice flour and chewiness of cooked rice, and could potentially be used as an important reference for rice ECQ evaluation. This study could help the applications of Wx loci in rice quality breeding.

Genetic Effects Analysis of QTLs for Rice Grain Size Based on CSSL-Z403 and Its Dissected Single and Dual-Segment Substitution Lines.

Rice chromosomal segment substitution lines (CSSLs) are ideal materials for studying quantitative traits such as grain size. Here, a rice large-grain CSSL-Z403 was identified among progeny of the recipient Xihui18 and the donor Jinhui35 based on molecular marker-assisted selection. Z403 carried 10 substitution segments with average length of 3.01 Mb. Then, a secondary F2 population derived from a cross between Xihui18 and Z403 was used to map quantitative trait loci (QTL) for grain size. Six QTLs distributed on chromosomes 5, 6, 7, 9 and 12 were detected. Finally four single-segment substitution lines (SSSLs) and two dual-segment substitution lines (DSSLs) carrying these target QTLs were constructed, and 10 novel QTLs were identified by four SSSLs. The large grain of Z403 was controlled at least by qGWT5, qGWT7, qGWT9 and qGWT12, and its grain weight was influenced through grain length QTL such as qGL5, qGL6, qGL9 and qGL12, as well as grain width QTL such as qGW5, qGW7, qGW9 and qGW12. Among 16 QTLs, four QTLs including qGL6, etc., might be novel compared with the reported documents. Again, positive or less negative epistatic effects between two non-allelic QTLs (additive effect > 0) may assist screening the genotype with larger grain size in further selection.

GS6.1 controls kernel size and plant architecture in rice.

A novel QTL GS6.1 increases yield per plant by controlling kernel size, plant architecture, and kernel filling in rice. Kernel size and plant architecture are critical agronomic traits that greatly influence kernel yield in rice. Using the single-segment substitution lines (SSSLs) with an indica cultivar Huajingxian74 as a recipient parent and American Jasmine as a donor parent, we identified a novel quantitative trait locus (QTL), named GS6.1. Near isogenic line-GS6.1 (NIL-GS6.1) produces long and narrow kernels by regulating cell length and width in the spikelet hulls, thus increasing the 1000-kernel weight. Compared with the control, the plant height, panicles per plant, panicle length, kernels per plant, secondary branches per panicle, and yield per plant of NIL-GS6.1 are increased. In addition, GS6.1 regulates the kernel filling rate. GS6.1 controls kernel size by modulating the transcription levels of part of EXPANSINs, kernel filling-related genes, and kernel size-related genes. These results indicate that GS6.1 might be beneficial for improving kernel yield and plant architecture in rice breeding by molecular design.

Fine mapping and candidate gene analysis of qFL-A12-5: a fiber length-related QTL introgressed from Gossypium barbadense into Gossypium hirsutum.

The fiber length-related qFL-A12-5 identified in CSSLs introgressed from Gossypium barbadense into Gossypium hirsutum was fine-mapped to an 18.8 kb region on chromosome A12, leading to the identification of the GhTPR gene as a potential regulator of cotton fiber length. Fiber length is a key determinant of fiber quality in cotton, and it is a key target of artificial selection for breeding and domestication. Although many fiber length-related quantitative trait loci have been identified, there are few reports on their fine mapping or candidate gene validation, thus hampering efforts to understand the mechanistic basis of cotton fiber development. Our previous study identified the qFL-A12-5 associated with superior fiber quality on chromosome A12 in the chromosome segment substitution line (CSSL) MBI7747 (BC4F3:5). A single segment substitution line (CSSL-106) screened from BC6F2 was backcrossed to construct a larger segregation population with its recurrent parent CCRI45, thus enabling the fine mapping of 2852 BC7F2 individuals using denser simple sequence repeat markers to narrow the qFL-A12-5 to an 18.8 kb region of the genome, in which six annotated genes were identified in Gossypium hirsutum. Quantitative real-time PCR and comparative analyses led to the identification of GH_A12G2192 (GhTPR) encoding a tetratricopeptide repeat-like superfamily protein as a promising candidate gene for qFL-A12-5. A comparative analysis of the protein-coding regions of GhTPR among Hai1, MBI7747, and CCRI45 revealed two non-synonymous mutations. The overexpression of GhTPR resulted in longer roots in Arabidopsis, suggesting that GhTPR may regulate cotton fiber development. These results provide a foundation for future efforts to improve cotton fiber length.

Identification, Fine Mapping and Application of Quantitative Trait Loci for Grain Shape Using Single-Segment Substitution Lines in Rice (Oryza sativa L.).

Quantitative trait loci (QTLs) and HQTL (heterosis QTLs) for grain shape are two major genetic factors of grain yield and quality in rice (Oryza sativa L.). Although many QTLs for grain shape have been reported, only a few are applied in production. In this study, 54 QTLs for grain shape were detected on 10 chromosomes using 33 SSSLs (single-segment substitution lines) and methods of statistical genetics. Among these, 23 exhibited significant positive additive genetic effects, including some novel QTLs, among which qTGW4-(1,2), qTGW10-2, and qTGW10-3 were three QTLs newly found in this study and should be paid more attention. Moreover, 26 HQTLs for grain shape were probed. Eighteen of these exhibited significant positive dominant genetic effects. Thirty-three QTLs for grain shape were further mapped using linkage analysis. Most of the QTLs for grain shape produced pleiotropic effects, which simultaneously controlled multiple appearance traits of grain shape. Linkage mapping of the F2 population derived from sub-single-segment substitution lines further narrowed the interval harbouring qTGW10-3 to 75.124 kb between PSM169 and RM25753. The candidate gene was identified and could be applied to breeding applications by molecular marker-assisted selection. These identified QTLs for grain shape will offer additional insights for improving grain yield and quality in rice breeding.

Grain shape is a factor affecting the stigma exsertion rate in rice.

Stigma exsertion rate (SER) is an index of outcrossing ability in rice and is a key trait of male sterile lines (MSLs) in hybrid rice. In this study, it was found that the maintainer lines carrying gs3 and gs3/gw8 showed higher SER. Single-segment substitution lines (SSSLs) carrying gs3, gw5, GW7 or gw8 genes for grain shape and gene pyramiding lines were used to reveal the relationship between grain shape and SER. The results showed that the grain shape regulatory genes had pleiotropic effects on SER. The SERs were affected by grain shapes including grain length, grain width and the ratio of length to width (RLW) not only in low SER background, but also in high SER background. The coefficients of determination (R2) between grain length and SER, grain width and SER, and grain RLW and SER were 0.78, 0.72, and 0.91 respectively. The grain RLW was the most important parameter affecting SER, and a larger grain RLW was beneficial to stigma exsertion. The pyramiding line PL-gs3/GW7/gw8 showed the largest grain RLW and the highest SER, which will be a fine breeding resource. Further research showed that the grain shape regulatory genes had pleiotropic effects on stigma shape, although the R2 values between grain shape and stigma shape, and stigma shape and SER were lower. Our results demonstrate that grain shape is a factor affecting SER in rice, in part by affecting stigma shape. This finding will be helpful for breeding MSLs with high SER in hybrid rice.

Identification, Interaction, Expression, and Function of QTLs on Leaf Numbers with Single-Segment Substitution Lines in Rice

Rice leaf is a solar panel of photosynthesis and determines the light energy utilization and yield of plants. Leaf numbers appear as S-type or parabola-type growth curves throughout their development. However, the ways in which the genes regulate the process of leaf numbers still remain poorly understood. This paper first identified five QTLs associated with leaf numbers using single-segment substitution lines (SSSLs). Then, the epistatic effects between double QTLs were estimated via the decomposition of the QTL polymerization effects. Additionally, further the expression patterns and functions for these five QTLs and their epistasis were revealed by the methodologies of conditional QTL mapping and functional QTL mapping, respectively. The five SSSLs were detected as having significant additive and/or dominant effects at one or more stages, all of which increased the leaf numbers, except for the negative additive effect of the first SSSL. Seven pairs of QTLs interacted each other via three or four epistatic components, with the opposite effects in the case of single genes, i.e., most epistatic effects were negative. The five QTLs expressed their effects mainly in three stages, namely within 14 days, from 28 days to 42 days, and from 49 days to 63 days after transplantation. Positive effects and negative interactions of the QTLs were observed in the early and the late stages, but opposite interactions were observed in the middle stage. Mainly, three functional parameters, including the inflexion point, the peak value, and the degradation rate, were regulated via the QTL effects and their opposite interactions. This paper uncovered the genetic rule of five QTLs on the leaf numbers, including the interaction, expression, and function features. The information will be helpful to understand the genetic mechanism for developmental traits.