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For Selected: Download Citations EndNote Ris BibTeX Toggle Thumbnails Select Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica (oryza sativa L.) in Northeast China XU Xin, YE Jun-hua, YANG Ying-ying, LI Ruo-si, LI Zhen, WANG Shan, SUN Yan-fei, ZHANG Meng-chen, XU Qun, FENG Yue, WEI Xing-hua, YANG Yao-long 2022, 21 (6): 1539-1550.   DOI: 10.1016/S2095-3119(21)63701-2 Abstract （388）      PDF in ScienceDirect       Milling and appearance quality are important contributors to rice grain quality.  Abundant genetic diversity and a suitable environment are crucial for rice improvement.  In this study, we investigated the milling and appearance quality-related traits in a panel of 200 japonica rice cultivars selected from Liaoning, Jilin and Heilongjiang provinces in Northeast China.  Pedigree assessment and genetic diversity analysis indicated that cultivars from Jilin harbored the highest genetic diversity among the three geographic regions.  An evaluation of grain quality indicated that cultivars from Liaoning showed superior milling quality, whereas cultivars from Heilongjiang tended to exhibit superior appearance quality.  Single- and multi-locus genome-wide association studies (GWAS) were conducted to identify loci associated with milling and appearance quality-related traits.  Ninety-nine significant single-nucleotide polymorphisms (SNPs) were detected.  Three common SNPs were detected using the mixed linear model (MLM), mrMLM, and FASTmrMLM methods.  Linkage disequilibrium decay was estimated and indicated three candidate regions (qBRR-1, qBRR-9 and qDEC-3) for further candidate gene analysis.  More than 300 genes were located in these candidate regions.  Gene Ontology (GO) analysis was performed to discover the potential candidate genes.  Genetic diversity analysis of the candidate regions revealed that qBRR-9 may have been subject to strong selection during breeding.  These results provide information that will be valuable for the improvement of grain quality in rice breeding. Reference | Related Articles | Metrics Select A locus TUTOU2, determines the panicle apical abortion phenotype of rice (Oryza sativa L.) in tutou2 mutant ZHU Zi-chao, LUO Sheng, LEI Bin, LI Xian-yong, CHENG Zhi-jun 2022, 21 (3): 621-630.   DOI: 10.1016/S2095-3119(20)63447-5 Abstract （163）      PDF in ScienceDirect       Rice panicle apical abortion (PAA) is a detrimental agronomic trait resulting in spikelet number reduction and yield loss.  To understand its underlying molecular mechanism, we identified one recessive PAA mutant tutou2 from the offspring of tissue cultures.  The mutation locus was finely mapped to a 75-kb interval on the long arm of chromosome 10.  Sequence analysis revealed a single nucleotide substitution of A to T at the 941 position of LOC_Os10g31910 in tutou2, resulting in an amino acid change from isoleucine to phenylalanine.  Complementation analysis showed that the degenerated panicle phenotype in tutou2 was rescued in the transgenic lines.  A phenotype similar to tutou2 can also be obtained by LOC_Os10g31910 knockout in wild-type rice.  These results suggested that LOC_Os10g31910 is the causative locus TUTOU2 responsible for the tutou2 PAA phenotype and probably also the locus of DEL1, previously documented as a leaf senescence gene.  The significant phenotypic differences between del1 and tutou2 suggest that the locus DEL1/TUTOU2 plays roles in both leaf and panicle development which were not considered fully in previous studies. Reference | Related Articles | Metrics Select The removal of nitrate reductase phosphorylation enhances tolerance to ammonium nitrogen deficiency in rice HAN Rui-cai, XU Zhi-rong, LI Chen-yan, Adnan Rasheed, PAN Xiao-hua, SHI Qing-hua, WU Zi-ming 2022, 21 (3): 631-643.   DOI: 10.1016/S2095-3119(20)63473-6 Abstract （235）      PDF in ScienceDirect       Nitrate reductase (NR) is a key enzyme for nitrogen assimilation in plants, and its activity is regulated by posttranslational phosphorylation.  To investigate the effects of dephosphorylation of the NIA1 protein on the growth and the physiological and biochemical characteristics of rice under different forms of nitrogen supplies, the phenotypes, nitrogen metabolism and reactive oxygen metabolism were measured in NIA1 phosphorylation site-directed mutant lines (S532D and S532A), an OsNia1 over-expression line (OE) and Kitaake (wild type, WT).  Compared with WT and OE, S532D and S532A have stronger nitrogen assimilation capacities.  When ammonium nitrate served as the nitrogen source, the plant heights, dry weights of shoots and chlorophyll (Chl) contents of S532D and S532A were lower than those of the WT and OE, whereas hydrogen peroxide (H2O2), malondialdehyde (MDA) and nitrite contents were higher.  When potassium nitrate served as the nitrogen source, the plant heights, dry weights of shoots and Chl contents of S532D and S532A were higher than those of the WT and OE, there were no significant differences in the contents of H2O2 and MDA in the leaves of the test materials, and the difference in nitrite contents among different lines decreased.  When ammonium sulfate served as the nitrogen source, there were no significant differences in the physiological indexes of the test materials, except NR activity.  Compared with ammonium nitrate and ammonium sulfate, the content of NH4+-N in the leaves of each plant was lower when potassium nitrate was used as the nitrogen source.  The qPCR results showed that OsGS and OsNGS1 were negatively regulated by downstream metabolites, and OsNrt2.2 was induced by nitrate.  In summary, when ammonium nitrate served as the nitrogen source, the weak growth of NIA1 phosphorylation site-directed mutant lines was due to the toxicity caused by the excessive accumulation of nitrite.  When potassium nitrate served as the nitrogen source, the assimilation rates of nitrate, nitrite and ammonium salt were accelerated in NIA1 phosphorylation site-directed mutant lines, which could provide more nitrogen nutrition and improve the tolerance of rice to ammonium nitrogen deficiency.  These results could provide a possible method to improve the efficiency of nitrogen utilization in rice under low-nitrogen conditions.   Reference | Related Articles | Metrics Select Reducing phosphorylation of nitrate reductase improves nitrate assimilation in rice HAN Rui-cai, LI Chen-yan, Adnan Rasheed, PAN Xiao-hua, SHI Qing-hua, WU Zi-ming 2022, 21 (1): 15-25.   DOI: 10.1016/S2095-3119(20)63386-X Abstract （158）      PDF in ScienceDirect       Nitrate reductase (NR) is an important enzyme for nitrate assimilation in plants, and post-translational phosphorylation regulates NR activity.  To evaluate the impact of the dephosphorylation of nitrate reductase 1 (NIA1) protein on NR activity, nitrogen metabolism and plant growth, NIA1 phosphorylation site directed mutant lines (S532D and S532A) and an OsNia1 over-expression line (OE) were constructed, and the phenotype, NIA1 protein and its phosphorylation level, NR activity, nitrate metabolism and reactive oxygen metabolism of the transgenic lines were analysed.  Exogenous NIA1 protein was not phosphorylated in S532D and S532A mutant lines, and their NR activities, activity states of NR and assimilation efficiencies of NO3–-N were higher than those in Kitaake (WT) and OE.  The changes in these physiological and biochemical indexes in the OE line were less than in S532D and S532A compared to WT.  These results suggest that the removal of transcriptional level control had little effect on nitrogen metabolism, but the removal of post-translational modification had a profound effect on it.  With the removal of NIA1 phosphorylation and the improvement in the nitrate assimilation efficiency, the plant height and chlorophyll content of S532D and S532A decreased and the hydrogen peroxide and malondialdehyde contents of rice seedlings increased, which may be related to the excessive accumulation of nitrite as an intermediate metabolite.  These results indicated that the phosphorylation of NR may be a self-protection mechanism of rice.  The reduced phosphorylation level of nitrate reductase improved the assimilation of nitrate, and the increased phosphorylation level reduced the accumulation of nitrite and prevented the toxic effects of reactive oxygen species in rice.  Reference | Related Articles | Metrics Select Characterization and fine mapping of RTMS10, a semi-dominant reverse thermo-sensitive genic male sterile locus in rice NI Jin-long, WANG De-zheng, NI Da-hu, SONG Feng-shun, YANG Jian-bo, YAO Da-nian 2022, 21 (2): 316-325.   DOI: 10.1016/S2095-3119(20)63563-8 Abstract （277）      PDF in ScienceDirect       The discovery and application of environment-sensitive genic male sterile (EGMS) rice germplasm provide an easy method for hybrid rice breeding and have made great contributions to hybrid rice production.  Typically, the photoperiod- and thermo-sensitive GMS (P/TGMS) lines utilized in two-line hybrid systems are male sterile under long day or/and high temperature but fertile under short day or/and low temperature conditions.  However, YannongS (YnS), a reverse TGMS (rTGMS) line, is sterile under low temperature (<29°C) and fertile under high temperature (>29.5°C).  Here, we report a genetic study on the rTGMS trait in YnS.  Interestingly, the F1 plants of the cross between YnS and a cultivar, L422, were male sterile at 22°C and completely fertile at 27°C.  Moreover, the segregation ratio of fertile and sterile individuals in YnS/L422 F2 populations changed from 1:3.05 to 2.95:1 when the ambient temperature increased, showing that the rTGMS trait exhibits semi-dominance in YnS.  We further found a locus on chromosome 10, termed RTMS10, which controls the rTGMS trait in YnS.  We then finely mapped RTMS10 to a ~68 kb interval between markers ID13116 and ID1318 by YnS/L422 BC6F2 populations.  A near iso-genic line (NIL) NL1 from the BC6F3 generation was developed and the pollen of NL1 became abnormal from the meiosis stage under low temperature.  In summary, we identified an rTGMS locus, RTMS10, and provided co-segregated markers, which could help to accelerate molecular breeding of rTGMS lines and better understand the rTGMS trait in rice. Reference | Related Articles | Metrics Select Prospects of utilization of inter-subspecific heterosis between indica and japonica rice ZHANG Gui-quan 2020, 19 (1): 1-10.   DOI: 10.1016/S2095-3119(19)62843-1 Abstract （179）      PDF in ScienceDirect       The Asian cultivated rice (Oryza sativa L.) grown worldwide is divided into two subspecies, indica and japonica.  It is well known that the heterosis of inter-subspecies is usually stronger than that of intra-subspecies.  Since the 1970s, indica hybrid rice, an intra-subspecific hybrid rice, has being widely used in China and even in the world.  However, the inter-subspecific hybrid rice between indica and japonica is still unavailable.  The major obstacle is the hybrid sterility of the inter-subspecies.  In recent decades, the genetic and molecular basis of indica-japonica hybrid sterility was understood more and more clearly.  Some breeding approaches for overcoming inter-subspecific hybrid sterility were proposed and used to develop the indica-japonica hybrid rice.  The updated understanding will offer new approaches for development of breeding lines for overcoming indica-japonica hybrid sterility, which facilitates developing of inter-subspecific hybrid rice. Reference | Related Articles | Metrics Select OsHemA gene, encoding glutamyl-tRNA reductase (GluTR) is essential for chlorophyll biosynthesis in rice (Oryza sativa) ZENG Zhao-qiong, LIN Tian-zi, ZHAO Jie-yu, ZHENG Tian-hui, XU Le-feng, WANG Yi-hua, LIU Ling-long, JIANG Ling, CHEN Sai-hua, WAN Jian-min 2020, 19 (3): 612-623.   DOI: 10.1016/S2095-3119(19)62710-3 Abstract （143）      PDF in ScienceDirect       Chlorophyll (Chl) biosynthesis is essential for photosynthesis and plant growth.  Glutamyl-tRNA reductase (GluTR) catalyzes glutamyl-tRNA into glutamate-1-semialdehyde (GSA) and initiates the chlorophyll biosynthesis.  Even though the main role of GluTR has been established, the effects caused by natural variations in its corresponding gene remain largely unknown.  Here, we characterized a spontaneous mutant in paddy field with Chl biosynthesis deficiency, designated as cbd1.  With intact thylakoid lamellar structure, the cbd1 plant showed light green leaves and reduced Chl and carotenoids (Cars) content significantly compared to the wild type.  By map-based gene cloning, the mutation was restricted within a 57-kb region on chromosome 10, in which an mPingA miniature inverted-repeat transposable element (MITE) inserted in the promoter region of OsHemA gene.  Both leaf color and the pigment contents in cbd1 were recovered in a complementation test, confirming OsHemA was responsible for the mutant phenotype.  OsHemA was uniquely predicted to encode GluTR and its expression level was dramatically repressed in cbd1.  Transient transformation in protoplasts demonstrated that GluTR localized in chloroplasts and a signal peptide exists in its N-terminus.  A majority of Chl biosynthesis genes, except for POR and CHLG, were down-regulated synchronously by the repression of OsHemA, suggesting that an attenuation occurred in the Chl biosynthesis pathway.  Interestingly, we found major agronomic traits involved in rice yield were statistically unaffected, except for the number of full grains per panicle was increased in cbd1.  Collectively, OsHemA plays an essential role in Chl biosynthesis in rice and its weak allele can adjust leaf color and Chls content without compromise to rice yield. Reference | Related Articles | Metrics Select Gene mapping and candidate gene analysis of aberrant-floral spikelet 1 (afs1) in rice (Oryza sativa L.) ZHANG Ting, YOU Jing, YU Guo-ling, ZHANG Yi, CHEN Huan, LI Yi-dan, YE Li, YAO Wan-yue, TU Yu-jie, LING Ying-hua, HE Guang-hua, LI Yun-feng 2020, 19 (4): 921-930.   DOI: 10.1016/S2095-3119(19)62847-9 Abstract （136）      PDF in ScienceDirect       The spikelet is a unique inflorescence structure in grasses.  However, the molecular mechanism that regulates its development remains unclear, and we therefore characterize a spikelet mutant of rice (Oryza sativa L.), aberrant-floral spikelet 1 (afs1), which was derived from treatment of Xinong 1B with ethyl methanesulfonate.  In the afs1 mutant, the spikelet developed an additional lemma-like organ alongside the other normally developed floral organs, and the paleae were degenerated to differing degrees with or without normally developed inner floral organs.  Genetic analysis revealed that the afs1 phenotype was controlled by a single recessive gene.  The AFS1 gene was mapped between the insertion/deletion (InDel) marker Indel19 and the simple sequence repeat marker RM16893, with a physical distance of 128.5 kb on chromosome 4.  Using sequence analysis, we identified the deletion of a 5-bp fragment and a transversion from G to A within LOC_Os04g32510/ LAX2, which caused early termination of translation in the afs1 mutant.  These findings suggest that AFS1 may be a new allele of LAX2, and is involved in the development of floral organs by regulating the expression of genes related to their development.  The above results provide a new view on the function of LAX2, which may also regulate the development of spikelets.   Reference | Related Articles | Metrics Select Identification of long-grain chromosome segment substitution line Z744 and QTL analysis for agronomic traits in rice MA Fu-ying, DU Jie, WANG Da-chuan, WANG Hui, ZHAO Bing-bing, HE Guang-hua, YANG Zheng-lin, ZHANG Ting, WU Ren-hong, ZHAO Fang-ming 2020, 19 (5): 1163-1169.   DOI: 10.1016/S2095-3119(19)62751-6 Abstract （119）      PDF in ScienceDirect       Length of grain affects the appearance, quality, and yield of rice.  A rice long-grain chromosome segment substitution line Z744, with Nipponbare as the recipient parent and Xihui 18 as the donor parent, was identified.  Z744 contains a total of six substitution segments distributed on chromosomes (Chrs.) 1, 2, 6, 7, and 12, with an average substitution length of 2.72 Mb.  The grain length, ratio of length to width, and 1 000-grain weight of Z744 were significantly higher than those in Nipponbare.  The plant height, panicle number, and seed-set ratio in Z744 were significantly lower than those in Nipponbare, but they were still 78.7 cm, 13.5 per plant, and 86.49%, respectively.  Furthermore, eight QTLs of different traits were identified in the secondary F2 population, constructed by Nipponbare and Z744 hybridization.  The grain weight of Z744 was controlled by two synergistic QTLs (qGWT1 and qGWT7) and two subtractive QTLs (qGWT2 and qGWT6), respectively.  The increase in the grain weight of Z744 was caused mainly by the increase in grain length.  Two QTLs were detected, qGL1 and qGL7-3, which accounted for 25.54 and 15.58% of phenotypic variation, respectively.  A Chi-square test showed that the long-grain number and the short-grain number were in accordance with the 3:1 separation ratio, which indicates that the long grain is dominant over the short-grain and Z744 was controlled mainly by the principal effect qGL1.  These results offered a good basis for further fine mapping of qGL1 and further dissection of other QTLs into single-segment substitution lines. Reference | Related Articles | Metrics Select Mapping quantitative trait loci associated with starch paste viscosity attributes by using double haploid populations of rice (Oryza sativa L.) Tahmina SHAR, SHENG Zhong-hua, Umed ALI, Sajid FIAZ, WEI Xiang-jin, XIE Li-hong, JIAO Gui-ai, Fahad ALI, SHAO Gao-neng, HU Shi-kai, HU Pei-song, TANG Shao-qing 2020, 19 (7): 1691-1703.   DOI: 10.1016/S2095-3119(19)62726-7 Abstract （127）      PDF in ScienceDirect       The paste viscosity attributes of starch, measured by rapid visco analyzer (RVA), are important factors for the evaluation of the cooking and eating qualities of rice in breeding programs.  To determine the genetic roots of the paste viscosity attributes of rice grains, quantitative trait loci (QTLs) associated with the paste viscosity attributes were mapped, using a double haploid (DH) population derived from Zhongjiazao 17 (YK17), a super rice variety, crossed with D50, a tropic japonica variety.  Fifty-four QTLs, for seven parameters of the RVA profiles, were identified in three planting seasons.  The 54 QTLs were located on all of the 12 chromosomes, with a single QTL explaining 5.99 to 47.11% of phenotypic variation.  From the QTLs identified, four were repeatedly detected under three environmental conditions and the other four QTLs were repeated under two environments.  Most of the QTLs detected for peak viscosity (PKV), trough viscosity (TV), cool paste viscosity (CPV), breakdown viscosity (BDV), setback viscosity (SBV), and peak time (PeT) were located in the interval of RM6775–RM3805 under all three environmental conditions, with the exception of pasting temperature (PaT).  For digenic interactions, eight QTLs with six traits were identified for additive×environment interactions in all three planting environments.  The epistatic interactions were estimated only for PKV, SBV and PaT.  The present study will facilitate further understanding of the genetic architecture of eating and cooking quality (ECQ) in the rice quality improvement program.   Reference | Related Articles | Metrics Select The breeding of japonica rice in northern China: An 11-year study (2006–2016) CUI Yue, ZHU Meng-meng, XU Zheng-jin, CHEN Wen-fu 2020, 19 (8): 1941-1946.   DOI: 10.1016/S2095-3119(19)62799-1 Abstract （172）      PDF in ScienceDirect       The world’s population is facing food shortages due to climate change and the competition for arable land between food and energy crops.  Many national and international projects to develop “super rice” cultivars were established in recent decades to attain a ‘third leap forward’ in rice production.  In order to evaluate the breeding process in northern China, an 11-year tracking survey of japonica rice breeding, which involved a total of 520 rice accessions and 67 test plots, was completed in this study.  The results showed that the yields of these accessions had increased stably, which was similar to control check varieties (CKs).  The breeding strategy reduced the panicle number and increased the grain number per panicle through an increase of spikelet density (number of grains per centimeter on the panicle).  This high spikelet density benefits not only the yield but also the blast resistance and amylose content.  At higher latitudes, the preferred rice accessions had slim grain shape and extended growth period.  In the middle latitudes among the test plots, the breeders focused on reducing the amylose content to improve the cooking quality of the rice accessions.  Yield and blast resistance were the two highest priorities during the breeding selection process.  The present study evaluated the breeding process in northern China during the last decade, which may lead to new insights into the future of rice breeding.   Reference | Related Articles | Metrics Select Transcriptome and metabolome profiling of unheading in F1 hybrid rice WANG Jie, WEI Shao-bo, WANG Chun-chao, Najeeb Ullah KHAN, ZHANG Zhan-ying, WANG Wen-sheng, ZHAO Xiu-qin, ZHANG Hong-liang, LI Zi-chao, GAO Yong-ming 2020, 19 (10): 2367-2382.   DOI: 10.1016/S2095-3119(19)62838-8 Abstract （141）      PDF in ScienceDirect       Heading date is a crucial agronomic trait.  However, rice usually delays heading due to the photoperiod, temperature, hormones or age.  The present research was conducted to analyze the mechanism controlling heading date in F1 hybrid rice.  We constructed two test-crossing populations using two introgression lines (ILs), P20 and P21 coming from SH527/FH838 as the male parent, respectively, and male sterile line Jin23A as the female parent.  Meanwhile, the F1 hybrids of H20, obtained by mating P20 with Jin23A and having no heading, and H21, from the crossing between P21 and Jin23A having normal heading, were both observed under long days.  Here, we analyzed the photoperiodic response of F1 hybrids by transcriptome and metabolome profiling.  The greater differences displayed in the transcriptome and the metabolome were caused by photoperiod (exogenous) instead of genes (endogenous).  The coping mechanism resulted from long days (LD) in H20, leading to differences in the circadian rhythm and glutathione metabolism relative to other samples.  The circadian oscillator and GSH/GSSG cycle typically regulate ROS homeostasis, and both of them are responsible for modulating ROS in H20 under LD condition.  Both circadian rhythm genes and the reported genes related to heading date function via the DHD1/OsMFT1-Ehd1-RFT1-OsMADS14/OsMADS18 pathway and the glutathione metabolism pathway by regulating oxidative reduction processes.  Both pathways are involved in the heading process and they interacted through the oxidative reduction process which was induced by photoperiod regulation, and all of them collectively modulated the heading process.  The results of this study will be helpful for unraveling the mechanism of F1 hybrid responses to unheading under LD condition. Reference | Related Articles | Metrics Select GraS is critical for chloroplast development and affects yield in rice  DU Zhi-xuan, HAO Hui-ying, HE Jin-peng, WANG Jian-ping, HUANG Zhou, XU Jie, FU Hai-hui, FU Jun-ru, HE Hao-hua 2020, 19 (11): 2603-2615.   DOI: 10.1016/S2095-3119(19)62859-5 Abstract （141）      PDF in ScienceDirect       Leaf color has been considered an important agronomic trait in rice (Oryza sativa L.) for a long time.  The changes in leaf color affect the yield of rice.  In this study, a green-revertible albino (graS) mutant was isolated from a 60Co-gamma-irradiated mutant pool of indica cultivar Guangzhan 63-4S.  The fine mapping indicated that graS mutant was mapped to chromosome 1, and was located in a confined region between markers ab134 and InDel 8 with genetic distances of 0.11 and 0.06 cM, respectively.  Based on the annotation results, four open reading frames (ORFs) were predicted in this region.  Sequence analysis revealed that LOC_Os01g55974 had a 2-bp nucleotide insertion (AA) in the coding region that led to premature termination at the 324th base.  Sequence analysis and expression analysis of related genes indicated that LOC_Os01g55974 is the candidate gene of GraS.  We studied the genome and protein sequences of LOC_Os01g55974, and the data showed that GraS contains a deoxycytidine deaminase domain, which was expressed ubiquitously in all tissues.  Further investigation indicated that GraS plays an essential role in the regulation of chloroplast biosynthesis, photosynthetic capacity and yield.  Moreover, leaf color mutant can be used as an effective marker for the purity of breeding and hybridization. Reference | Related Articles | Metrics Select Breeding of CMS maintainer lines through anther culture assisted by high-resolution melting-based markers WANG Ping, BAI Yu-lu, WANG Min-xia, HU Bin-hua, PU Zhi-gang, ZHANG Zhi-yong, ZHANG Qiong, XU Deng-wu, LUO Wen-long, CHEN Zhi-qiang 2020, 19 (12): 2965-2973.   DOI: 10.1016/S2095-3119(20)63179-3 Abstract （103）      PDF in ScienceDirect       The integrated use of molecular marker-assisted selection (MAS) and anther culture has potential to significantly increase efficiency in plant breeding; however, reports on this kind of practical use are very limited.  In the present study, we report the development of cytoplasmic male sterile (CMS) maintainers with aroma, disease resistance and red-brown hulls, as an example of integration of MAS and anther culture in rice breeding.  A high-resolution melting (HRM)-based functional molecular marker was developed for the red-brown hull trait caused by a unique mutation (rbh1) in OsCAD2.  Functional molecular markers for genes of rice blast resistance (Pi2), aroma (fgr) and red-brown hull (rbh1) were used for precise genotyping of individual plants in the BC1 and BC2F2 populations derived from a cross between CMS maintainers Huaxiang B (pi2–/rbh1–/fgr–) and Rong 3B (Pi2+/RBH1+/Fgr+).  A total of 89 doubled haploid (DH) lines were generated from selected BC2F2 plants (Pi2+/rbh1–/fgr–) by anther culture.  Seven DH lines were subsequently selected as the potential new CMS maintainers based on their overall performance and high resistance to blast.  Our study demonstrated that integration of MAS and anther culture significantly accelerated the development of CMS maintainers with multiple stacked genes. Reference | Related Articles | Metrics Select Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding REN Yun, CHEN Dan, LI Wen-jie, TAO Luo, YUAN Guo-qiang, CAO Ye, LI Xue-mei, DENG Qi-ming, WANG Shi-quan, ZHENG Ai-ping, ZHU Jun, LIU Huai-nian, WANG Ling-xia, LI Ping, LI Shuang-cheng 2021, 20 (1): 35-45.   DOI: 10.1016/S2095-3119(20)63256-7 Abstract （228）      PDF in ScienceDirect       Hybrid rice significantly contributes to the food supply worldwide.  Backbone parents play important roles in elite hybrid rice breeding systems.  In this study, we performed pedigree-based analysis of the elite backbone parent rice variety, namely, Shuhui 527 (SH527, Oryza sativa), to exploit key genome regions during breeding.  Twenty-four cultivars (including SH527, its six progenitors and 17 derived cultivars) were collected and analyzed with high-density single nucleotide polymorphism (SNP) array.  Scanning all these cultivars with genome-wide SNP data indicated the unique contributions of progenitors to the SH527 genome and identified the key genomic regions of SH527 conserved within all its derivatives.  These findings were further supported by known rice yield-related genes or unknown QTLs identified by genome-wide association study.  This study reveals several key regions for SH527 and provides insights into hybrid rice breeding.   Reference | Related Articles | Metrics Select Receptor-like kinase OsASLRK regulates methylglyoxal response and content in rice LIN Fa-ming, LI Shen, WANG Ke, TIAN Hao-ran, GAO Jun-feng, DU Chang-qing 2021, 20 (7): 1731-1742.   DOI: 10.1016/S2095-3119(20)63258-0 Abstract （132）      PDF in ScienceDirect       Receptor-like kinases (RLKs) are essential for plant abiotic stress responses.  Methylglyoxal (MG) is a cellular metabolite that is often considered to be a stress signal molecule.  However, limited information is available about the relationship between RLKs and MG.  Here, we addressed the function of a receptor-like kinase, OsASLRK, in the MG response and content in rice.  A typical MG-responsive element (AAAAAAAA) exists in the promoter region of the OsASLRK gene.  RT-qPCR analysis indicated that the transcript level of OsASLRK was significantly increased by exogenous MG in a time- and dosage-dependent fashion.  GUS staining also confirmed that the expression of OsASLRK in rice root was enhanced by exogenous MG treatment.  Genetic analysis suggested that the Osaslrk mutant displays increased sensitivity to MG and it showed higher endogenous MG content under exogenous MG treatments, while OsASLRK-overexpressing rice plants showed the opposite phenotypes.  Diaminobenzidine (DAB) staining, scavenging enzyme activities and GSH content assays indicate that OsASLRK regulates MG sensitivity and content via the elevation of antioxidative enzyme activities and alleviation of membrane damage.  Therefore, our results provide new evidence illustrating the roles that receptor-like kinase OsASLRK plays in MG regulation in rice. Reference | Related Articles | Metrics Select A rice geranylgeranyl reductase is essential for chloroplast development LIU Xi, YI Xin, YANG Yan-rong, HUANG Qian-qian 2021, 20 (10): 2592-2600.   DOI: 10.1016/S2095-3119(20)63324-X Abstract （120）      PDF in ScienceDirect       Chloroplasts are essential for plant photosynthesis and growth. Many genes have been identified that regulate plant chloroplast development. However, it is not known at a molecular level how these genes regulate chloroplast biogenesis. In this study, we isolated a mutant ygl2 (yellow-green leaf2) that exhibited a pigment-defective phenotype. YGL2 encodes a geranylgeranyl reductase, and in mutant ygl2, there was a single base change (T1361G) located in the third exon of YGL2 that resulted in a missense mutation (L454R) in the encoded product. Transmission electron microscopy revealed that chloroplast development was impaired in the ygl2 mutant. The expression levels of plastid-encoded genes were significantly altered in the ygl2 mutant. Furthermore, in a yeast two-hybrid assay, we found that YGL2 interacted with the RNA editing factor MORF8. Reference | Related Articles | Metrics Select Transgenic japonica rice expressing the cry1C gene is resistant to striped stem borers in Northeast China JIN Yong-mei, MA Rui, YU Zhi-jing, LIN Xiu-feng 2021, 20 (11): 2837-2848.   DOI: 10.1016/S2095-3119(20)63279-8 Abstract （161）      PDF in ScienceDirect       Rice production and quality are seriously affected by the lepidopteran pest, striped stem borer (SSB), in Northeast China. In this study, a synthetic cry1C gene encoding Bacillus thuringiensis (Bt) δ-endotoxin, which is toxic to lepidopteran pest, was transformed into a japonica rice variety (Jigeng 88) in Northeast China by Agrobacterium-mediated transformation.  Through molecular detection and the Basta resistance germination assay, a total of 16 single-copy homozygous transgenic lines were obtained from 126 independent transformants expressing cry1C.  Finally, four cry1C-transgenic lines (JL16, JL23, JL41, and JL42) were selected by evaluation of the Cry1C protein level, insect-resistance and agronomic traits.  The cry1C-transgenic lines had higher resistance to SSB and higher yield compared with non-transgenic (NT) control plants.  T-DNA flanking sequence analysis of the transgenic line JL42 showed that the cry1C gene was inserted into the intergenic region of chromosome 11, indicating that its insertion may not interfere with the genes near insertion site.  In summary, this study developed four cry1C-transgenic japonica rice lines with high insect resistance and high yield.  They can be used as insect-resistant germplasm materials to overcome the problem of rice yield reduction caused by SSB and reduce the use of pesticides in Northeast China. Reference | Related Articles | Metrics Select Less hairy leaf 1, an RNaseH-like protein, regulates trichome formation in rice through auxin CHEN Hong-yan, ZHU Zhu, WANG Xiao-wen, LI Yang-yang, HU Dan-ling, ZHANG Xue-fei, JIA Lu-qi, CUI Zhi-bo, SANG Xian-chun 2023, 22 (1): 31-40.   DOI: 10.1016/j.jia.2022.08.101 Abstract （498）      PDF in ScienceDirect       The trichomes of rice leaves are formed by the differentiation and development of epidermal cells.  Plant trichomes play an important role in stress resistance and protection against direct ultraviolet irradiation.  However, the development of rice trichomes remains poorly understood.  In this study, we conducted ethylmethane sulfonate (EMS)-mediated mutagenesis on the wild-type (WT) indica rice ‘Xida 1B’.  Phenotypic analysis led to the screening of a mutant that is defective in trichome development, designated lhl1 (less hairy leaf 1).  We performed map-based cloning and localized the mutated gene to the 70-kb interval between the molecular markers V-9 and V-10 on chromosome 2.  The locus LOC_Os02g25230 was identified as the candidate gene by sequencing.  We constructed RNA interference (LHL1-RNAi) and overexpression lines (LHL1-OE) to verity the candidate gene.  The leaves of the LHL1-RNAi lines showed the same trichome developmental defects as the lhl1 mutant, whereas the trichome morphology on the leaf surface of the LHL1-OE lines was similar to that of the WT, although the number of trichomes was significantly higher.  Quantitative real-time PCR (RT-qPCR) analysis revealed that the expression levels of auxin-related genes and positive regulators of trichome development in the lhl1 mutant were down-regulated compared with the WT.  Hormone response analysis revealed that LHL1 expression was affected by auxin.  The results indicate that the influence of LHL1 on trichome development in rice leaves may be associated with an auxin pathway. Reference | Related Articles | Metrics Select OsMas1, a novel maspardin protein gene, confers tolerance to salt and drought stresses by regulating ABA signaling in rice WANG Fei-bing, WAN Chen-zhong, NIU Hao-fei, QI Ming-yang, LI Gang, ZHANG Fan, HU Lai-bao, YE Yu-xiu, WANG Zun-xin, PEI Bao-lei, CHEN Xin-hong, YUAN Cai-yuan 2023, 22 (2): 341-359.   DOI: 10.1016/j.jia.2022.08.077 Abstract （370）      PDF in ScienceDirect       Drought and salt stresses, the major environmental abiotic stresses in agriculture worldwide, affect plant growth, crop productivity, and quality.  Therefore, developing crops with higher drought and salt tolerance is highly desirable.  This study reported the isolation, biological function, and molecular characterization of a novel maspardin gene, OsMas1, from rice.  The OsMas1 protein was localized to the cytoplasm.  The expression levels of OsMas1 were up-regulated under mannitol, PEG6000, NaCl, and abscisic acid (ABA) treatments in rice.  The OsMas1 gene was introduced into the rice cultivar Zhonghua 11 (wild type, WT).  OsMas1-overexpression (OsMas1-OE) plants exhibited significantly enhanced salt and drought tolerance; in contrast, OsMas1-interference (OsMas1-RNAi) plants exhibited decreased tolerance to salt and drought stresses, compared with WT.  OsMas1-OE plants exhibited enhanced hypersensitivity, while OsMas1-RNAi plants showed less sensitivity to exogenous ABA treatment at both germination and post-germination stages.  ABA, proline and K+ contents and superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and photosynthesis activities were significantly increased.  In contrast, malonaldehyde (MDA), hydrogen peroxide (H2O2), superoxide anion radical (O2-·), and Na+ contents were significantly decreased in OsMas1-OE plants compared with OsMas1-RNAi and WT plants.  Overexpression of OsMas1 up-regulated the genes involved in ABA signaling, proline biosynthesis, reactive oxygen species (ROS)-scavenging system, photosynthesis, and ion transport under salt and drought stresses.  Our results indicate that the OsMas1 gene improves salt and drought tolerance in rice, which may serve as a candidate gene for enhancing crop resistance to abiotic stresses. Reference | Related Articles | Metrics Select Analyses and identifications of quantitative trait loci and candidate genes controlling mesocotyl elongation in rice ZHANG Xi-juan, LAI Yong-cai, MENG Ying, TANG Ao, DONG Wen-jun, LIU You-hong, LIU Kai, WANG Li-zhi, YANG Xian-li, WANG Wen-long, DING Guo-hua, JIANG Hui, REN Yang, JIANG Shu-kun 2023, 22 (2): 325-340.   DOI: 10.1016/j.jia.2022.08.080 Abstract （599）      PDF in ScienceDirect       Rice direct seeding has the significant potential to save labor and water, conserve environmental resources, and reduce greenhouse gas emissions tremendously.  Therefore, rice direct seeding is becoming the major cultivation technology applied to rice production in many countries.  Identifying and utilizing genes controlling mesocotyl elongation is an effective approach to accelerate breeding procedures and meet the requirements for direct-seeded rice (DSR) production.  This study used a permanent mapping population with 144 recombinant inbred lines (RILs) and 2 828 bin-markers to detect quantitative trait loci (QTLs) associated with mesocotyl length in 2019 and 2020.  The mesocotyl lengths of the rice RILs and their parents, Lijiangxintuanheigu (LTH) and Shennong 265 (SN265), were measured in a growth chamber at 30°C in a dark environment.  A total of 16 QTLs for mesocotyl length were identified on chromosomes 1(2), 2(4), 3(2), 4, 5, 6, 7, 9, 11(2), and 12.  Seven of these QTLs, including qML1a, qML1b, qML2d, qML3a, qML3b, qML5, and qML11b, were reproducibly detected in both years via the interval mapping method.  The major QTL, qML3a, was reidentified in two years via the composite interval mapping method.  A total of 10 to 413 annotated genes for each QTL were identified in their smallest genetic intervals of 37.69 kb to 2.78 Mb, respectively.  Thirteen predicted genes within a relatively small genetic interval (88.18 kb) of the major mesocotyl elongation QTL, qML3a, were more thoroughly analyzed.  Finally, the coding DNA sequence variations among SN265, LTH, and Nipponbare indicated that the LOC_Os03g50550 gene was the strongest candidate gene for the qML3a QTL controlling the mesocotyl elongation.  This LOC_Os03g50550 gene encodes a mitogen-activated protein kinase.  Relative gene expression analysis using qRT-RCR further revealed that the expression levels of the LOC_Os03g50550 gene in the mesocotyl of LTH were significantly lower than in the mesocotyl of SN265.  In conclusion, these results further strengthen our knowledge about rice’s genetic mechanisms of mesocotyl elongation.  This investigation’s discoveries will help to accelerate breeding programs for new DSR variety development. Reference | Related Articles | Metrics Select Development of new aromatic rice lines with high eating and cooking qualities Kanokwan KAEWMUNGKUN, Keasinee TONGMARK, Sriprapai CHAKHONKAEN, Numphet SANGARWUT, Thiwawan WASINANON, Natjaree PANYAWUT, Khanittha DITTHAB, Kannika SIKAEWTUNG, QI Yong-bin, Sukanya DAPHA, Atikorn PANYA, Natthaporn PHONSATTA, Amorntip MUANGPROM 2023, 22 (3): 679-690.   DOI: 10.1016/j.jia.2022.07.001 Abstract （238）      PDF in ScienceDirect       Rice is the staple food for about half of the world’s population.  Preferred by consumers, aromatic rice is a special type of rice with great commercial value.  Cooking and eating qualities and aroma are the major grain qualities favored by most consumers.  Currently, most of the available aromatic varieties have low yields and some undesirable agronomic traits.  Thus, there is an urgent need to develop better aromatic rice varieties.  This work aims to identify rice germplasm lines that have good grain quality and to develop new varieties with desirable traits.  Thirty-six out of 188 germplasm lines were found to have betaine aldehyde dehydrogenase 2 (badh2) controlling the aroma and were analyzed for their 2-acetyl-1-pyrroline (2AP) contents.  Then, 17 of those lines were found to have alleles for low amylose content and low gelatinization temperature, controlled by waxy and starch synthase IIa (SSIIa), respectively, suggesting that they are aromatic rice lines with high cooking and eating qualities.  A total of 158 F7 recombinant inbred lines (RILs) generated from five crosses of the selected germplasm lines were planted for phenotypic and yield observations, resulting in 27 F8 RILs selected for yield evaluation and genotyping.  Finally, four out of the seven F9 aromatic RILs showed high yield, high 2AP production, and low amylose content, in agreement with their genotypes.  The other three F9 RILs were aromatic rice lines with high amylose content and high yield.  Because consumer preferences for grain quality vary depending on regions and ethnic groups, the high-yielding aromatic RILs generated from this study can be used to increase the yield of Thai rice and to raise market value and farm profits. Reference | Related Articles | Metrics Select OsDXR interacts with OsMORF1 to regulate chloroplast development and the RNA editing of chloroplast genes in rice CAO Peng-hui, WANG Di, GAO Su, LIU Xi, QIAO Zhong-ying, XIE Yu-lin, DONG Ming-hui, DU Tan-xiao, ZHANG Xian, ZHANG Rui, JI Jian-hui 2023, 22 (3): 669-678.   DOI: 10.1016/j.jia.2022.08.005 Abstract （378）      PDF in ScienceDirect       Plant chlorophyll biosynthesis and chloroplast development are two complex processes that are regulated by exogenous and endogenous factors.  In this study, we identified OsDXR, a gene encoding a reductoisomerase that positively regulates chlorophyll biosynthesis and chloroplast development in rice.  OsDXR knock-out lines displayed the albino phenotype and could not complete the whole life cycle process.  OsDXR was highly expressed in rice leaves, and subcellular localization indicated that OsDXR is a chloroplast protein.  Many genes involved in chlorophyll biosynthesis and chloroplast development were differentially expressed in the OsDXR knock-out lines compared to the wild type.  Moreover, we found that the RNA editing efficiencies of ndhA-1019 and rpl2-1 were significantly reduced in the OsDXR knock-out lines.  Furthermore, OsDXR interacted with the RNA editing factor OsMORF1 in a yeast two-hybrid screen and bimolecular fluorescence complementation assay.  Finally, disruption of the plastidial 2-C-methyl-derythritol-4-phosphate pathway resulted in defects in chloroplast development and the RNA editing of chloroplast genes. Reference | Related Articles | Metrics Select OsPPR9 encodes a DYW-type PPR protein that affects editing efficiency of multiple RNA editing sites and is essential for chloroplast development CHEN Chang-zhao, WANG Ya-Liang, HE Meng-xing, LI Zhi-wen, SHEN Lan, LI Qing, RE De-yong, HU Jiang, ZHU Li, ZHANG Guang-heng, GAO Zhen-yu, ZENG Da-li, GUO Long-biao, QIAN Qian, ZHANG Qiang 2023, 22 (4): 972-980.   DOI: 10.1016/j.jia.2022.08.026 Abstract （334）      PDF in ScienceDirect       Photosynthesis occurs mainly in chloroplasts, whose development is regulated by proteins encoded by nuclear genes.  Among them, pentapeptide repeat (PPR) proteins participate in organelle RNA editing.  Although there are more than 450 members of the PPR protein family in rice, only a few affect RNA editing in rice chloroplasts.  Gene editing technology has created new rice germplasm and mutants, which could be used for rice breeding and gene function study.  This study evaluated the functions of OsPPR9 in chloroplast RNA editing in rice.  The osppr9 mutants were obtained by CRISPR/Cas9, which showed yellowing leaves and a lethal phenotype, with suppressed expression of genes associated with chloroplast development and accumulation of photosynthetic-related proteins.  In addition, loss of OsPPR9 protein function reduces the editing efficiency of rps8-C182, rpoC2-C4106, rps14-C80, and ndhB-C611 RNA editing sites, which affects chloroplast growth and development in rice.  Our data showed that OsPPR9 is highly expressed in rice leaves and encodes a DYW-PPR protein localized in chloroplasts.  Besides, the OsPPR9 protein was shown to interact with OsMORF2 and OsMORF9.  Together, our findings provide insights into the role of the PPR protein in regulating chloroplast development in rice.  Reference | Related Articles | Metrics Select OsNPF3.1, a nitrate, abscisic acid and gibberellin transporter gene, is essential for rice tillering and nitrogen utilization efficiency Junnan Hang, Bowen Wu, Diyang Qiu, Guo Yang, Zhongming Fang, Mingyong Zhang 2024, 23 (4): 1087-1104.   DOI: 10.1016/j.jia.2023.04.024 Abstract （513）      PDF in ScienceDirect       Low-affinity nitrate transporter genes have been identified in subfamilies 4–8 of the rice nitrate transporter 1 (NRT1)/peptide transporter family (NPF), but the OsNPF3 subfamily responsible for nitrate and phytohormone transport and rice growth and development remains unknown.  In this study, we described OsNPF3.1 as an essential nitrate and phytohormone transporter gene for rice tillering and nitrogen utilization efficiency (NUtE).  OsNPF3.1 possesses four major haplotypes of its promoter sequence in 517 cultivars, and its expression is positively associated with tiller number.  Its expression was higher in the basal part, culm, and leaf blade than in other parts of the plant, and was strongly induced by nitrate, abscisic acid (ABA) and gibberellin 3 (GA3) in the root and shoot of rice.  Electrophysiological experiments demonstrated that OsNPF3.1 is a pH-dependent low-affinity nitrate transporter, with rice protoplast uptake assays showing it to be an ABA and GA3 transporter.  OsNPF3.1 overexpression significantly promoted ABA accumulation in the roots and GA accumulation in the basal part of the plant which inhibited axillary bud outgrowth and rice tillering, especially at high nitrate concentrations.  The NUtE of OsNPF3.1-overexpressing plants was enhanced under low and medium nitrate concentrations, whereas the NUtE of OsNPF3.1 clustered regularly interspaced short palindromic repeats (CRISPR) plants was increased under high nitrate concentrations.  The results indicate that OsNPF3.1 transports nitrate and phytohormones in different rice tissues under different nitrate concentrations.  The altered OsNPF3.1 expression improves NUtE in the OsNPF3.1-overexpressing and CRISPR lines at low and high nitrate concentrations, respectively. Reference | Related Articles | Metrics Select Artificial selection of the Green Revolution gene Semidwarf 1 is implicated in upland rice breeding Shuliang Jiao, Qinyan Li, Fan Zhang, Yonghong Tao, Yingzhen Yu, Fan Yao, Qingmao Li, Fengyi Hu, Liyu Huang 2024, 23 (3): 769-780.   DOI: 10.1016/j.jia.2023.05.010 Abstract （255）      PDF in ScienceDirect       Semidwarf breeding has boosted crop production and is a well-known outcome from the first Green Revolution.  The Green Revolution gene Semidwarf 1 (SD1), which modulates gibberellic acid (GA) biosynthesis, plays a principal role in determining rice plant height.  Mutations in SD1 reduce rice plant height and promote lodging resistance and fertilizer tolerance to increase grain production.  The plant height mediated by SD1 also favors grain yield under certain conditions.  However, it is not yet known whether the function of SD1 in upland rice promotes adaptation and grain production.  In this study, the plant height and grain yield of irrigated and upland rice were comparatively analyzed under paddy and dryland conditions.  In response to dryland environments, rice requires a reduction in plant height to cope with water deficits.  Upland rice accessions had greater plant heights than their irrigated counterparts under both paddy and dryland conditions, and appropriately reducing plant height could improve adaptability to dryland environments and maintain high grain yield formation.  Moreover, upland rice cultivars with thicker stem diameters had stronger lodging resistance, which addresses the lodging problem.  Knockout of SD1 in the upland rice cultivar IRAT104 reduced the plant height and grain yield, demonstrating that the adjustment of plant height mediated by SD1 could increase grain production in dryland fields.  In addition, an SD1 genetic diversity analysis verified that haplotype variation causes phenotypic variation in plant height.  During the breeding history of rice, SD1 allelic mutations were selected from landraces to improve the grain yield of irrigated rice cultivars, and this selection was accompanied by a reduction in plant height.  Thus, five known mutant alleles were analyzed to verify that functional SD1 is required for upland rice production.  All these results suggest that SD1 might have undergone artificial positive selection in upland rice, which provides further insights concerning greater plant height in upland rice breeding. Reference | Related Articles | Metrics Select The auxin transporter OsAUX1 regulates tillering in rice (Oryza sativa) Luqi Jia, Yongdong Dai, Ziwei Peng, Zhibo Cui, Xuefei Zhang, Yangyang Li, Weijiang Tian, Guanghua He, Yun Li, Xianchun Sang 2024, 23 (5): 1454-1467.   DOI: 10.1016/j.jia.2023.05.041 Abstract （247）      PDF in ScienceDirect       Tillering is an important agronomic trait of rice (Oryza sativa) that affects the number of effective panicles, thereby affecting yields.  The phytohormone auxin plays a key role in tillering.  Here we identified the high tillering and semi-dwarf 1 (htsd1) mutant with auxin-deficiency root characteristics, such as shortened lateral roots, reduced lateral root density, and enlarged root angles.  htsd1 showed reduced sensitivity to auxin, but the external application of indole-3-acetic acid (IAA) inhibited its tillering.  We identified the mutated gene in htsd1 as AUXIN1 (OsAUX1, LOC_Os01g63770), which encodes an auxin influx transporter.  The promoter sequence of OsAUX1 contains many SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) binding sites, and we demonstrated that SPL7 binds to the OsAUX1 promoter.  TEOSINTE BRANCHED1 (OsTB1), a key gene that negatively regulates tillering, was significantly downregulated in htsd1.  Tillering was enhanced in the OsTB1 knockout mutant, and the external application of IAA inhibited tiller elongation in this mutant.  Overexpressing OsTB1 restored the multi-tiller phenotype of htsd1.  These results suggest that SPL7 directly binds to the OsAUX1 promoter and regulates tillering in rice by altering OsTB1 expression to modulate auxin signaling. Reference | Related Articles | Metrics Select Natural variation in the cytochrome c oxidase subunit 5B OsCOX5B regulates seed vigor by altering energy production in rice Chengwei Huang, Zhijuan Ji, Qianqian Huang, Liling Peng, Wenwen Li, Dandan Wang, Zepeng Wu, Jia Zhao, Yongqi He, Zhoufei Wang 2024, 23 (9): 2898-2910.   DOI: 10.1016/j.jia.2023.06.018 Abstract （211）      PDF in ScienceDirect       Seed vigor is a crucial trait for the direct seeding of rice.  Here we examined the genetic regulation of seed vigor traits in rice, including germination index (GI) and germination potential (GP), using a genome-wide association study approach.  One major quantitative trait locus, qGI6/qGP6, was identified simultaneously for both GI and GP.  The candidate gene encoding the cytochrome c oxidase subunit 5B (OsCOX5B) was validated for qGI6/qGP6.  The disruption of OsCOX5B caused the vigor traits to be significantly lower in Oscox5b mutants than in the japonica Nipponbare wild type (WT).  Gene co-expression analysis revealed that OsCOX5B influences seed vigor mainly by modulating the tricarboxylic acid cycle process.  The glucose levels were significantly higher while the pyruvic acid and adenosine triphosphate levels were significantly lower in Oscox5b mutants than in WT during seed germination.  The elite haplotype of OsCOX5B facilitates seed vigor by increasing its expression during seed germination.  Thus, we propose that OsCOX5B is a potential target for the breeding of rice varieties with enhanced seed vigor for direct seeding. Reference | Related Articles | Metrics Select SUPER WOMAN 2 (SPW2) maintains organ identity in spikelets by inhibiting the expression of floral homeotic genes OsMADS3, OsMADS58, OsMADS13, and DROOPING LEAF ZHUANG Hui, LAN Jin-song, YANG Qiu-ni, ZHAO Xiao-yu, LI Yu-huan, ZHI Jing-ya, SHEN Ya-lin, HE Guang-hua, LI Yun-feng 2024, 23 (1): 59-76.   DOI: 10.1016/j.jia.2023.07.010 Abstract （292）      PDF in ScienceDirect       Flower organ identity in rice is mainly determined by the A-, B-, C- and E-class genes, with the majority encoding MADS-box transcription factors.  However, few studies have investigated how the expression of these floral organ identity genes is regulated during flower development.  In this study, we identified a gene named SUPER WOMAN 2 (SPW2), which is necessary for spikelet/floret development in rice by participating in the regulation of the expression of pistil identity genes such as OsMADS3, OsMADS13, OsMADS58 and DL.  In the spw2 mutant, ectopic stigma/ovary-like tissues were observed in the non-pistil organs, including sterile lemma, lemma, palea, lodicule, and stamen, suggesting that the identities of these organs were severely affected by mutations in SPW2.  SPW2 was shown to encode a plant-specific EMF1-like protein that is involved in H3K27me3 modification as an important component of the PRC2 complex.  Expression analysis showed that the SPW2 mutation led to the ectopic expression of OsMADS3, OsMADS13, OsMADS58, and DL in non-pistil organs of the spikelet.  The ChIP-qPCR results showed significant reductions in the levels of H3K27me3 modification on the chromatin of these genes.  Thus, we demonstrated that SPW2 can mediate the process of H3K27me3 modification of pistil-related genes to regulate their expression in non-pistil organs of spikelets in rice.  The results of this study expand our understanding of the molecular mechanism by which SPW2 regulates floral organ identity genes through epigenetic regulation. Reference | Related Articles | Metrics Select Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice Xiaogang He, Zirong Li, Sicheng Guo, Xingfei Zheng, Chunhai Liu, Zijie Liu, Yongxin Li, Zheming Yuan, Lanzhi Li 2024, 23 (8): 2541-2556.   DOI: 10.1016/j.jia.2023.07.021 Abstract （181）      PDF in ScienceDirect       Marker-assisted selection (MAS) and genomic selection (GS) breeding have greatly improved the efficiency of rice breeding.  Due to the influences of epistasis and gene pleiotropy, ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.  In this study, 113 indica rice varieties (V) and their 565 testcross hybrids (TC) were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.  The original traits and general combining ability of the parents, as well as the original traits and mid-parent heterosis of TC, were subjected to genome-wide association analysis.  In total, 381 primary significantly associated loci (SAL) and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.  Among these loci, 322 candidate genes located within or nearby the SALs were screened, 204 of which were cloned genes.  A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.  All the SALs were used to construct genetic networks, in which 91 pleiotropic loci were investigated.  Additionally, we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs, primary SALs, secondary SALs or epistatic effect SALs as covariates.  Although the prediction accuracies of the four models were generally not significantly different in the TC dataset, the incorporation of primary SALs, secondary SALs, and epistatic effect SALs significantly improved the prediction accuracies of 5 (26%), 3 (16%), and 11 (58%) traits in the V dataset, respectively.  These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.  They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice. Reference | Related Articles | Metrics Select Genetic analysis and fine mapping of a grain size QTL in the small-grain sterile rice line Zhuo201S Bin Lei, Jiale Shao, Feng Zhang, Jian Wang, Yunhua Xiao, Zhijun Cheng, Wenbang Tang, Jianmin Wan 2024, 23 (7): 2155-2163.   DOI: 10.1016/j.jia.2023.07.026 Abstract （286）      PDF in ScienceDirect       The development and application of the small-grain rice sterile line Zhuo201S (Z201S) has demonstrated its potential for mechanized hybrid rice seed production, leading to significant cost reductions.  However, the molecular mechanism responsible for the small-grain size characteristic of Z201S remains unclear.  In this study, we conducted a genetic analysis using near-isogenic lines constructed from Z210S, a small-grain rice sterile line, and R2115, a normal-grain variety.  The results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain number.  Through mapping, we localized the causal gene to the short arm of chromosome 2, within a 113 kb physical region delimited by the molecular markers S2-4-1 and LB63.  Transgenic analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene, suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified. Reference | Related Articles | Metrics Select Exploring the genetic basis of pre-harvest sprouting in rice through a genome-wide association study-based haplotype analysis Myeong-Hyeon Min, Aye Aye Khaing, Sang-Ho Chu, Bhagwat Nawade, Yong-Jin Park 2024, 23 (8): 2525-2540.   DOI: 10.1016/j.jia.2023.12.004 Abstract （113）      PDF in ScienceDirect       In this study, we employed genome-wide association studies (GWAS) on diverse rice accessions to identify novel PHS-associated haplotypes.  An assessment of 127 cultivated accessions for panicle germination (PHS) and detached grain germination (germination rate of detached grains at the 14th day (D14)) revealed considerable phenotypic variation among rice ecotypes.  GWAS analysis identified 91 significant signals at –log10(P-value)>5, including 15 SNPs for PHS and 76 SNPs for D14.  A subsequent linkage disequilibrium (LD) block-based GWAS analysis detected 227 significant SNPs for both traits, consisting of 18 nonsynonymous substitutions located on the coding regions of nine genes.  Further haplotype analysis identified 32 haplotypes, with 10 specific to cultivated accessions, 19 specific to the wild type, and three shared between them.  A phenotypic assessment of major haplotypes revealed significant differences between resistant (Hap1 and Hap2) and susceptible haplotypes (Hap5, Hap27, and Hap28), distinguished by a G/A SNP within a novel gene, Os04g0545200.  The identified haplotypes offer promising prospects for haplotype-based breeding aimed at enhancing PHS resistance in rice. 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