Rice最新文献

{"title":"Temperature Effect on Rhizome Development in Perennial rice.","authors":"Kai Wang, Jie Li, Yourong Fan, Jiangyi Yang","doi":"10.1186/s12284-024-00710-2","DOIUrl":"10.1186/s12284-024-00710-2","url":null,"abstract":"<p><p>Traditional agriculture is becoming increasingly not adapted to global climate change. Compared with annual rice, perennial rice has strong environmental adaptation and needs fewer natural resources and labor inputs. Rhizome, a kind of underground stem for rice to achieve perenniallity, can grow underground horizontally and then bend upward, developing into aerial stems. The temperature has a great influence on plant development. To date, the effect of temperature on rhizome development is still unknown. Fine temperature treatment of Oryza longistaminata (OL) proved that compared with higher temperatures (28-30 ℃), lower temperature (17-19 ℃) could promote the sprouting of axillary buds and enhance negative gravitropism of branches, resulting in shorter rhizomes. The upward growth of branches was earlier at low temperature than that at high temperature, leading to a high frequency of shorter rhizomes and smaller branch angles. Comparative transcriptome showed that plant hormones played an essential role in the response of OL to temperature. The expressions of ARF17, ARF25 and FucT were up-regulated at low temperature, resulting in prospectively asymmetric auxin distribution, which subsequently induced asymmetric expression of IAA20 and WOX11 between the upper and lower side of the rhizome, further leading to upward growth of the rhizome. Cytokinin and auxin are phytohormones that can promote and inhibit bud outgrowth, respectively. The auxin biosynthesis gene YUCCA1 and cytokinin oxidase/dehydrogenase gene CKX4 and CKX9 were up-regulated, while cytokinin biosynthesis gene IPT4 was down-regulated at high temperature. Moreover, the D3 and D14 in strigolactones pathways, negatively regulating bud outgrowth, were up-regulated at high temperature. These results indicated that cytokinin, auxins, and strigolactones jointly control bud outgrowth at different temperatures. Our research revealed that the outgrowth of axillary bud and the upward growth of OL rhizome were earlier at lower temperature, providing clues for understanding the rhizome growth habit under different temperatures, which would be helpful for cultivating perennial rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"32"},"PeriodicalIF":5.5,"publicationDate":"2024-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11078906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140877252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Supplementation of Jasmonic acid Mitigates the Damaging Effects of Arsenic Stress on Growth, Photosynthesis and Nitrogen Metabolism in Rice","authors":"Houneida Attia, Khalid H. Alamer","doi":"10.1186/s12284-024-00709-9","DOIUrl":"https://doi.org/10.1186/s12284-024-00709-9","url":null,"abstract":"<p>Experiments were conducted to evaluate the role of exogenously applied jasmonic acid (JA; 0.1 and 0.5 µM) in alleviating the toxic effects of arsenic (As; 5 and 10 µM) stress in rice. Plants treated with As showed considerable decline in growth attributes like height, fresh and dry weight of plant. Arsenic stress reduced the content of δ-amino livulenic acid (δ-ALA), glutamate 1-semialdehyde (GSA), total chlorophylls and carotenoids, with more reduction evident at higher (10 µM) As concentrations, however exogenously supplied JA alleviated the decline to considerable extent. Arsenic stress mediated decline in photosynthetic gas exchange parameters, Fv/Fm (PSII activity) and Rubisco activity was alleviated by the exogenous treatment of JA. Arsenic stress caused oxidative damage which was evident as increased lipid peroxidation, lipoxygenase activity and hydrogen peroxide concentrations however, JA treatment declined these parameters. Treatment of JA improved the activity of nitrate reductase and glutamate synthase under unstressed conditions and also alleviated the decline triggered by As stress. Activity of antioxidant enzymes assayed increased due to As stress, and the supplementation of JA caused further increase in their activities. Moreover, the content of proline, free amino acids and total phenols increased significantly due to JA application under stressed and unstressed conditions. Treatment of JA increased the content of nitrogen and potassium while as reduced As accumulation significantly.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"19 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140805221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Allantoate Amidohydrolase OsAAH is Essential for Preharvest Sprouting Resistance in Rice","authors":"Ting Xie, Wenling Hu, Jiaxin Shen, Jiangyu Xu, Zeyuan Yang, Xinyi Chen, Peiwen Zhu, Mingming Chen, Sunlu Chen, Hongsheng Zhang, Jinping Cheng","doi":"10.1186/s12284-024-00706-y","DOIUrl":"https://doi.org/10.1186/s12284-024-00706-y","url":null,"abstract":"<p>Preharvest sprouting (PHS) is an undesirable trait that decreases yield and quality in rice production. Understanding the genes and regulatory mechanisms underlying PHS is of great significance for breeding PHS-resistant rice. In this study, we identified a mutant, <i>preharvest sprouting 39</i> (<i>phs39</i>), that exhibited an obvious PHS phenotype in the field. MutMap⁺ analysis and transgenic experiments demonstrated that <i>OsAAH</i>, which encodes allantoate amidohydrolase, is the causal gene of <i>phs39</i> and is essential for PHS resistance. <i>OsAAH</i> was highly expressed in roots and leaves at the heading stage and gradually increased and then weakly declined in the seed developmental stage. OsAAH protein was localized to the endoplasmic reticulum, with a function of hydrolyzing allantoate in vitro. Disruption of <i>OsAAH</i> increased the levels of ureides (allantoate and allantoin) and activated the tricarboxylic acid (TCA) cycle, and thus increased energy levels in developing seeds. Additionally, the disruption of <i>OsAAH</i> significantly increased asparagine, arginine, and lysine levels, decreased tryptophan levels, and decreased levels of indole-3-acetic acid (IAA) and abscisic acid (ABA). Our findings revealed that the OsAAH of ureide catabolism is involved in the regulation of rice PHS via energy and hormone metabolisms, which will help to facilitate the breeding of rice PHS-resistant varieties.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"53 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Spatial Distribution and Characteristics of Protein Content and Composition in Japonica Rice Grains: Implications for Sake Quality","authors":"Kei Takahashi, Hiromi Kohno, Masaki Okuda","doi":"10.1186/s12284-024-00708-w","DOIUrl":"https://doi.org/10.1186/s12284-024-00708-w","url":null,"abstract":"<p>The quantity and composition of rice proteins play a crucial role in determining taste quality of <i>sake</i>, Japanese rice wine. However, the spatial distribution of proteins within rice grains, especially in endosperm tissue, and the differences between rice varieties remain unclear. Here, we analyzed the crude protein contents and composition ratios of table (<i>Nipponbare</i> and <i>Koshihikari</i>) and genuine sake rice varieties (<i>Yamadanishiki</i>, <i>Gohyakumangoku</i>, <i>Dewasansan</i>, <i>Dewanosato</i>, and <i>Yumenokaori</i>) to elucidate their spatial distribution within the Japonica rice grain endosperm. Seven sake rice varieties were polished over five harvest years using a brewer’s rice-polishing machine. We obtained fractions at 90–70% (the outermost endosperm fraction), 70–50%, 50–30%, and 30–0% (the central region of the endosperm fraction). <i>Yamadanishiki</i> and <i>Dewanosato</i> exhibited considerably lower crude protein contents than the other cultivars. After applying SDS-PAGE, the protein composition, comprising glutelin/total protein (G/TP), prolamin/TP (P/TP), and G/P ratios of these fractions was determined. In white rice (at a 90% rice-polishing ratio), the average ratio of the major protein composition was G/TP 41%, P/TP 21%, and G/P ratios of 1.97. <i>Gohyakumangoku</i> and <i>Yamadanishiki</i> had higher G/TP ratio, while <i>Dewanosato</i> had a lower value. Despite having lower crude protein contents, <i>Yamadanishiki</i> and <i>Dewanosato</i> exhibited significantly varying G/TP ratios. The G/TP ratio markedly varied among rice varieties, particularly in the rice grains’ central region. The 50–30% fraction had the highest P/TP ratio among all tested rice varieties, suggesting spatial differences in P/TP within rice grains. <i>Koshihikari</i> had the lowest P/TP ratio. In addition, the 50–30% fraction had the lowest G/P ratio among all tested rice varieties, with <i>Gohyakumangoku</i> having the highest G/P ratio. <i>Dewanosato</i> had the lowest G/P value, and this value significantly differed from that of <i>Yamadanishiki</i> in the 30–0% fraction. We found substantial differences in protein composition within distinct spatial regions of rice grains, and larger differences among rice varieties were observed in the rice grain’s central region.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"14 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pangenome-Wide Association Study and Transcriptome Analysis Reveal a Novel QTL and Candidate Genes Controlling both Panicle and Leaf Blast Resistance in Rice","authors":"Jian Wang, Haifei Hu, Xianya Jiang, Shaohong Zhang, Wu Yang, Jingfang Dong, Tifeng Yang, Yamei Ma, Lian Zhou, Jiansong Chen, Shuai Nie, Chuanguang Liu, Yuese Ning, Xiaoyuan Zhu, Bin Liu, Jianyuan Yang, Junliang Zhao","doi":"10.1186/s12284-024-00707-x","DOIUrl":"https://doi.org/10.1186/s12284-024-00707-x","url":null,"abstract":"<p>Cultivating rice varieties with robust blast resistance is the most effective and economical way to manage the rice blast disease. However, rice blast disease comprises leaf and panicle blast, which are different in terms of resistance mechanisms. While many blast resistant rice cultivars were bred using genes conferring resistance to only leaf or panicle blast, mining durable and effective quantitative trait loci (QTLs) for both panicle and leaf blast resistance is of paramount importance. In this study, we conducted a pangenome-wide association study (panGWAS) on 9 blast resistance related phenotypes using 414 international diverse rice accessions from an international rice panel. This approach led to the identification of 74 QTLs associated with rice blast resistance. One notable locus, <i>qPBR1</i>, validated in a F_4:5 population and fine-mapped in a Heterogeneous Inbred Family (HIF), exhibited broad-spectrum, major and durable blast resistance throughout the growth period. Furthermore, we performed transcriptomic analysis of 3 resistant and 3 sensitive accessions at different time points after infection, revealing 3,311 differentially expressed genes (DEGs) potentially involved in blast resistance. Integration of the above results identified 6 candidate genes within the <i>qPBR1</i> locus, with no significant negative effect on yield. The results of this study provide valuable germplasm resources, QTLs, blast response genes and candidate functional genes for developing rice varieties with enduring and broad-spectrum blast resistance. The <i>qPBR1</i>, in particular, holds significant potential for breeding new rice varieties with comprehensive and durable resistance throughout their growth period.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"36 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140584648","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Case Study from the Overexpression of OsTZF5, Encoding a CCCH Tandem Zinc Finger Protein, in Rice Plants Across Nineteen Yield Trials","authors":"Alexandre Grondin, Mignon A. Natividad, Takuya Ogata, Asad Jan, Amélie C. M. Gaudin, Kurniawan R. Trijatmiko, Evelyn Liwanag, Kyonoshin Maruyama, Yasunari Fujita, Kazuko Yamaguchi-Shinozaki, Kazuo Nakashima, Inez H. Slamet-Loedin, Amelia Henry","doi":"10.1186/s12284-024-00705-z","DOIUrl":"https://doi.org/10.1186/s12284-024-00705-z","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Background</h3><p>Development of transgenic rice overexpressing transcription factors involved in drought response has been previously reported to confer drought tolerance and therefore represents a means of crop improvement. We transformed lowland rice IR64 with <i>OsTZF5</i>, encoding a CCCH-tandem zinc finger protein, under the control of the rice <i>LIP9</i> stress-inducible promoter and compared the drought response of transgenic lines and nulls to IR64 in successive screenhouse paddy and field trials up to the T₆ generation.</p><h3 data-test=\"abstract-sub-heading\">Results</h3><p>Compared to the well-watered conditions, the level of drought stress across experiments varied from a minimum of − 25 to − 75 kPa at a soil depth of 30 cm which reduced biomass by 30–55% and grain yield by 1–92%, presenting a range of drought severities. <i>OsTZF5</i> transgenic lines showed high yield advantage under drought over IR64 in early generations, which was related to shorter time to flowering, lower shoot biomass and higher harvest index. However, the increases in values for yield and related traits in the transgenics became smaller over successive generations despite continued detection of drought-induced transgene expression as conferred by the <i>LIP9</i> promoter. The decreased advantage of the transgenics over generations tended to coincide with increased levels of homozygosity. Background cleaning of the transgenic lines as well as introgression of the transgene into an IR64 line containing major-effect drought yield QTLs, which were evaluated starting at the BC₃F₁ and BC₂F₃ generation, respectively, did not result in consistently increased yield under drought as compared to the respective checks.</p><h3 data-test=\"abstract-sub-heading\">Conclusions</h3><p>Although we cannot conclusively explain the genetic factors behind the loss of yield advantage of the transgenics under drought across generations, our results help in distinguishing among potential drought tolerance mechanisms related to effectiveness of the transgenics, since early flowering and harvest index most closely reflected the levels of yield advantage in the transgenics across generations while reduced biomass did not.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"21 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583530","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OsCRLK2, a Receptor-Like Kinase Identified by QTL Analysis, is Involved in the Regulation of Rice Quality","authors":"Ying Chen, Hanfeng Shi, Guili Yang, Xueyu Liang, Xiaolian Lin, Siping Tan, Tao Guo, Hui Wang","doi":"10.1186/s12284-024-00702-2","DOIUrl":"https://doi.org/10.1186/s12284-024-00702-2","url":null,"abstract":"<p>The quality of rice (<i>Oryza sativa</i> L) is determined by a combination of appearance, flavor, aroma, texture, storage characteristics, and nutritional composition. Rice quality directly influences acceptance by consumers and commercial value. The genetic mechanism underlying rice quality is highly complex, and is influenced by genotype, environment, and chemical factors such as starch type, protein content, and amino acid composition. Minor variations in these chemical components may lead to substantial differences in rice quality. Among these components, starch is the most crucial and influential factor in determining rice quality. In this study, quantitative trait loci (QTLs) associated with eight physicochemical properties related to the rapid viscosity analysis (RVA) profile were identified using a high-density sequence map constructed using recombinant inbred lines (RILs). Fifty-nine QTLs were identified across three environments, among which <i>qGT6.4</i> was a novel locus co-located across all three environments. By integrating RNA-seq data, we identified the differentially expressed candidate gene <i>OsCRLK2</i> within the <i>qGT6.4</i> interval. <i>osclrk2</i> mutants exhibited decreased gelatinization temperature (GT), apparent amylose content (AAC) and viscosity, and increased chalkiness. Furthermore, <i>osclrk2</i> mutants exhibited downregulated expression of the majority of starch biosynthesis-related genes compared to wild type (WT) plants. In summary, <i>OsCRLK2</i>, which encodes a receptor-like protein kinase, appears to consistently influence rice quality across different environments. This discovery provides a new genetic resource for use in the molecular breeding of rice cultivars with improved quality.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"20 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583657","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Mediator Subunit OsMED16 Interacts with the WRKY Transcription Factor OsWRKY45 to Enhance Rice Resistance Against Magnaporthe oryzae.","authors":"Yanfei Wu, Yuquan Fu, Zhonglin Zhu, Qin Hu, Feng Sheng, Xuezhu Du","doi":"10.1186/s12284-024-00698-9","DOIUrl":"10.1186/s12284-024-00698-9","url":null,"abstract":"<p><p>Rice blast, caused by Magnaporthe oryzae (M. oryzae), is one of the most common and damaging diseases of rice that limits rice yield and quality. The mediator complex plays a vital role in promoting transcription by bridging specific transcription factors and RNA polymerase II. Here, we show that the rice mediator subunit OsMED16 is essential for full induction of the diterpenoid phytoalexin biosynthesis genes and resistance to the ascomycetous fungus M. oryzae. Mutants of Osmed16 show reduced expression of the DP biosynthesis genes and are markedly more susceptible to M. oryzae, while transgenic plants overexpressing OsMED16 increased the expression of the DP biosynthesis genes and significantly enhanced resistance to M. oryzae. Interestingly, OsMED16 is physically associated with the WRKY family transcription factor OsWRKY45, which interacts with the phytoalexin synthesis key regulator transcription factor OsWRKY62. Further, OsMED16-OsWRKY45-OsWRKY62 complex could bind to the promoter regions of phytoalexin synthesis-related genes and activate their gene expression. Our results show that OsMED16 may enhance rice tolerance to M. oryzae via directly manipulating phytoalexin de novo biosynthesis.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"23"},"PeriodicalIF":5.5,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10984912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140336791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study.","authors":"Julia García-Romeral, Raúl Castanera, Josep Casacuberta, Concha Domingo","doi":"10.1186/s12284-024-00701-3","DOIUrl":"10.1186/s12284-024-00701-3","url":null,"abstract":"<p><p>Allelopathy has been considered as a natural method of weed control. Despite the nature of allelochemical compounds has been studied, little is known about the genetic basis underlying allelopathy. However, it is known that rice exhibits diverse allelopathic potentials across varieties, and breeding for rice plants exhibiting allelopathic potential conferring an advantage against weeds in paddy fields would be highly desirable. Knowledge of the gene factors and the identification of the genomic regions responsible for allelopathy would facilitate breeding programs. Taking advantage of the existing genetic diversity in rice, particularly in temperate japonica rice, we conducted a comprehensive investigation into the genetic determinants that contribute to rice allelopathy. Employing Genome-Wide Association Study, we identified four Quantitative Trait Loci, with the most promising loci situated on chromosome 2 and 5. Subsequent inspection of the genes located within these QTLs revealed genes associated with the biosynthesis of secondary metabolites such as Phenylalanine Ammonia Lyase (PAL), a key enzyme in the synthesis of phenolic compounds, and two genes coding for R2R3-type MYB transcription factors. The identification of these two QTLs associated to allelopathy in rice provides a useful tool for further exploration and targeted breeding strategies.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"22"},"PeriodicalIF":4.8,"publicationDate":"2024-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10965883/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140294453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits.","authors":"Puranjoy Sar, Sonal Gupta, Motilal Behera, Koushik Chakraborty, Umakanta Ngangkham, Bibhash Chandra Verma, Amrita Banerjee, Prashantkumar S Hanjagi, Debarati Bhaduri, Sandip Shil, Jitendra Kumar, Nimai Prasad Mandal, Paresh Chandra Kole, Michael D Purugganan, Somnath Roy","doi":"10.1186/s12284-024-00700-4","DOIUrl":"10.1186/s12284-024-00700-4","url":null,"abstract":"<p><p>The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"17 1","pages":"20"},"PeriodicalIF":5.5,"publicationDate":"2024-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10963711/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140288896","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}