RicePub Date : 2023-12-15DOI: 10.1186/s12284-023-00677-6
Fallou Seck, Giovanny Covarrubias-Pazaran, Tala Gueye, Jérôme Bartholomé
{"title":"Realized Genetic Gain in Rice: Achievements from Breeding Programs","authors":"Fallou Seck, Giovanny Covarrubias-Pazaran, Tala Gueye, Jérôme Bartholomé","doi":"10.1186/s12284-023-00677-6","DOIUrl":"https://doi.org/10.1186/s12284-023-00677-6","url":null,"abstract":"<p>Genetic improvement is crucial for ensuring food security globally. Indeed, plant breeding has contributed significantly to increasing the productivity of major crops, including rice, over the last century. Evaluating the efficiency of breeding strategies necessitates a quantification of this progress. One approach involves assessing the genetic gain achieved through breeding programs based on quantitative traits. This study aims to provide a theoretical understanding of genetic gain, summarize the major results of genetic gain studies in rice breeding, and suggest ways of improving breeding program strategies and future studies on genetic gain. To achieve this, we present the concept of genetic gain and the essential aspects of its estimation. We also provide an extensive literature review of genetic gain studies in rice (<i>Oryza sativa</i> L.) breeding programs to understand the advances made to date. We reviewed 29 studies conducted between 1999 and 2023, covering different regions, traits, periods, and estimation methods. The genetic gain for grain yield, in particular, showed significant variation, ranging from 1.5 to 167.6 kg/ha/year, with a mean value of 36.3 kg/ha/year. This translated into a rate of genetic gain for grain yield ranging from 0.1% to over 3.0%. The impact of multi-trait selection on grain yield was clarified by studies that reported genetic gains for other traits, such as plant height, days to flowering, and grain quality. These findings reveal that while breeding programs have achieved significant gains, further improvements are necessary to meet the growing demand for rice. We also highlight the limitations of these studies, which hinder accurate estimations of genetic gain. In conclusion, we offer suggestions for improving the estimation of genetic gain based on quantitative genetic principles and computer simulations to optimize rice breeding strategies.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"34 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138682953","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}
RicePub Date : 2023-12-13DOI: 10.1186/s12284-023-00676-7
Lin Zhu, Faliang Zeng, Yinpei Liang, Qi Wang, Hongwei Chen, Pulin Feng, Mingqian Fan, Yanshuang Cheng, Jiayu Wang
{"title":"Small Papillae Regulated by SPD25 are Critical for Balancing Photosynthetic CO2 Assimilation and Water Loss in Rice","authors":"Lin Zhu, Faliang Zeng, Yinpei Liang, Qi Wang, Hongwei Chen, Pulin Feng, Mingqian Fan, Yanshuang Cheng, Jiayu Wang","doi":"10.1186/s12284-023-00676-7","DOIUrl":"https://doi.org/10.1186/s12284-023-00676-7","url":null,"abstract":"<h3 data-test=\"abstract-sub-heading\">Background</h3><p>The leaf epidermis plays an important role in the transmission of light and the regulation of water and gas exchange, which influences the photosynthesis of mesophyll cells. Small papillae (SP) are one of the important structural elements of the leaf epidermis. The mechanism of the effect that small papillae have on rice leaf photosynthetic performance remains unclear.</p><h3 data-test=\"abstract-sub-heading\">Results</h3><p>In this study, a <i>small papilla deficient 25</i> (<i>spd25</i>) mutant was isolated from <i>japonica</i> rice Longjin1. Small papillae were absent on the adaxial and abaxial leaf surfaces of the <i>spd25</i> mutant and the silicon and cuticular wax content in the <i>spd25</i> mutant leaves decreased. Map-based cloning and functional analysis revealed that <i>SPD25</i>, encoding a guanine nucleotide exchange factor for Rop, is a novel allele of <i>OsRopGEF10</i>. The <i>spd25</i> mutant showed an increased water loss rate and reduced relative water content. The lower stomatal conductance in the <i>spd25</i> mutant prevented water loss but decreased the intercellular CO<sub>2</sub> concentration and net assimilation rate. The fluorescence parameters showed that the inhibited CO<sub>2</sub> assimilation reaction feedback regulated the photochemical electron-transfer reaction, but the performance of Photosystem II was stable. Further analysis indicated that the excess light energy absorbed by the <i>spd25</i> mutant was dissipated in the form of non-photochemical quenching to avoid photodamage through the optical properties of small papillae.</p><h3 data-test=\"abstract-sub-heading\">Conclusions</h3><p><i>SPD25</i> regulates the development of small papillae on the surface of rice leaves, which play an important role in balancing photosynthetic gas exchange and water loss. This study deepens our understanding of the physiological mechanisms by which small papillae affect photosynthetic performance.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"288 1 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138631969","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}
RicePub Date : 2023-12-13DOI: 10.1186/s12284-023-00674-9
Tao Lu, Wenjin Yin, Yinuo Zhang, Chaoyu Zhu, Qianqian Zhong, Sanfeng Li, Nuo Wang, Zhengai Chen, Hanfei Ye, Yuan Fang, Dan Mu, Yuexing Wang, Yuchun Rao
{"title":"WLP3 Encodes the Ribosomal Protein L18 and Regulates Chloroplast Development in Rice","authors":"Tao Lu, Wenjin Yin, Yinuo Zhang, Chaoyu Zhu, Qianqian Zhong, Sanfeng Li, Nuo Wang, Zhengai Chen, Hanfei Ye, Yuan Fang, Dan Mu, Yuexing Wang, Yuchun Rao","doi":"10.1186/s12284-023-00674-9","DOIUrl":"https://doi.org/10.1186/s12284-023-00674-9","url":null,"abstract":"<p>Plastid ribosomal proteins play a crucial role in the growth and development of plants, mainly in the gene expression and translation of key genes in chloroplasts. While some information is known about the regulatory processes of plastid ribosomal proteins in various plant species, there is limited knowledge about the underlying mechanisms in rice. In this study, ethyl methanesulfonate (EMS) mutagenesis was used to generate a new mutant called <i>wlp3</i> (<i>white leaf and panicle3</i>), characterized by white or albino leaves and panicles, which exhibited this phenotype from the second leaf stage until tillering. Furthermore, after a certain period, the newly emerging leaves developed the same phenotype as the rice variety ZH11, while the albino leaves of <i>wlp3</i> showed an incomplete chloroplast structure and significantly low chlorophyll content. A transition mutation (T to C) at position 380 was identified in the coding region of the <i>LOC_Os03g61260</i> gene, resulting in the substitution of isoleucine by threonine during translation. <i>WLP3</i> encodes the ribosomal L18 subunit, which is localized in the chloroplast. Complementation experiments confirmed that <i>LOC_Os03g61260</i> was responsible for the albino phenotype in rice. <i>WLP3</i> has high expression in the coleoptile, leaves at the three-leaf stage, and panicles at the heading stage. Compared to the wild-type (WT), <i>wlp3</i> exhibited reduced chlorophyll synthesis and significantly decreased expression levels of genes associated with plastid development. Yeast two-hybrid (Y2H) analysis revealed that WLP3 interacts with other ribosomal subunits, to influence chloroplast development. These results contribute to a better understanding of the underlying molecular mechanisms of chloroplast development and plastid gene translation.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"104 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138631728","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}
RicePub Date : 2023-12-13DOI: 10.1186/s12284-023-00673-w
Suk-Hwan Kim, Jungwon Yoon, Hanna Kim, Sang-Ji Lee, Nam-Chon Paek
{"title":"Rice Basic Helix-Loop-Helix 079 (OsbHLH079) Delays Leaf Senescence by Attenuating ABA Signaling","authors":"Suk-Hwan Kim, Jungwon Yoon, Hanna Kim, Sang-Ji Lee, Nam-Chon Paek","doi":"10.1186/s12284-023-00673-w","DOIUrl":"https://doi.org/10.1186/s12284-023-00673-w","url":null,"abstract":"<p>Leaf senescence represents the final phase of leaf development and is characterized by a highly organized degenerative process involving the active translocation of nutrients from senescing leaves to growing tissues or storage organs. To date, a large number of senescence-associated transcription factors (sen-TFs) have been identified that regulate the initiation and progression of leaf senescence. Many of these TFs, including NAC (NAM/ATAF1/2/CUC2), WRKY, and MYB TFs, have been implicated in modulating the expression of downstream senescence-associated genes (SAGs) and chlorophyll degradation genes (CDGs) under the control of phytohormones. However, the involvement of basic helix-loop-helix (bHLH) TFs in leaf senescence has been less investigated. Here, we show that <i>OsbHLH079</i> delays both natural senescence and dark-induced senescence: Overexpression of <i>OsbHLH079</i> led to a stay-green phenotype, whereas <i>osbhlh079</i> knockout mutation displayed accelerated leaf senescence. Similar to other sen-TFs, <i>OsbHLH079</i> showed a gradual escalation in expression as leaves underwent senescence. During this process, the mRNA levels of SAGs and CDGs remained relatively low in <i>OsbHLH079</i> overexpressors, but increased sharply in <i>osbhlh079</i> mutants, suggesting that <i>OsbHLH079</i> negatively regulates the transcription of SAGs and CDGs under senescence conditions. Additionally, we found that <i>OsbHLH079</i> delays ABA-induced senescence. Subsequent RT-qPCR and dual-luciferase reporter assays revealed that OsbHLH079 downregulates the expression of ABA signaling genes, such as <i>OsABF2</i>, <i>OsABF4</i>, <i>OsABI5</i>, and <i>OsNAP</i>. Taken together, these results demonstrate that <i>OsbHLH079</i> functions in delaying leaf yellowing by attenuating the ABA responses.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138631982","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":"HCC1, a Polygalacturonase, Regulates Chlorophyll Degradation via the Ethylene Synthesis Pathway","authors":"Yongxiang Liao, Bing Xiang, Zhenzhen Xue, Asif Ali, Yong Li, Mengyuan Li, Aiji Wei, Jialu Xin, Daiming Guo, Yingxiu Liao, Yunfeng Tian, Zhixue Zhao, Peizhou Xu, Hongyu Zhang, Xiaoqiong Chen, Yutong Liu, Hao Zhou, Duo Xia, Kangxi Du, Xianjun Wu","doi":"10.1186/s12284-023-00675-8","DOIUrl":"https://doi.org/10.1186/s12284-023-00675-8","url":null,"abstract":"<p>Chlorophyll degradation is an important physiological process and is essential for plant growth and development. However, how chlorophyll degradation is controlled at the cellular and molecular level remains largely elusive. Pectin is a main component of the primary cell wall, and polygalacturonases (PGs) is a group of pectin-hydrolases that cleaves the pectin backbone and release oligogalacturonide. Whether and how PGs affect chlorophyll degradation metabolism and its association with ethylene (ETH) have not been reported before. Here, we report a novel function of PG in a mutant ‘<i>high chlorophyll content1’ hcc1</i>, which displayed a decrease in growth and yield. Our morphological, biochemical and genetic analyses of <i>hcc1</i>, knockout lines and complementation lines confirm the function of <i>HCC1</i> in chlorophyll degradation. In <i>hcc1</i>, the PG activity, ETH content and D-galacturonic acid (D-GA) was significantly decreased and showed an increase in the thickness of the cell wall. Exogenous application of ETH and D-GA can increase ETH content and induce the expression of <i>HCC1</i>, which further can successfully induce the chlorophyll degradation in <i>hcc1</i>. Together, our data demonstrated a novel function of <i>HCC1</i> in chlorophyll degradation via the ETH pathway.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2023-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138563559","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}
RicePub Date : 2023-12-08DOI: 10.1186/s12284-023-00670-z
Zhufeng Chen, Jianxin Wu, Xing Wang Deng, Xiaoyan Tang
{"title":"Establishment and Advances of Third-Generation Hybrid Rice Technology: A Review","authors":"Zhufeng Chen, Jianxin Wu, Xing Wang Deng, Xiaoyan Tang","doi":"10.1186/s12284-023-00670-z","DOIUrl":"https://doi.org/10.1186/s12284-023-00670-z","url":null,"abstract":"<p>Rice (<i>Oryza sativa</i> L.) is one of the most important food crops worldwide. The utilisation of heterosis (hybrid vigour) has played a significant role in increasing rice yield and ensuring food supply. Over the past 50 years, the first-generation three-line system based on cytoplasmic male sterility, and the second-generation two-line system based on environment-sensitive genic male sterility (EGMS), have been widely applied in hybrid rice production. However, the three-line system is restricted by the matching relationship among the three parental lines and allows only ~ 2–5% of germplasms to be explored for elite combinations. The environmental sensitivity of EGMS lines has posed serious risks to the production of hybrid seeds. These factors have hindered the development and applications of hybrid rice. Third-generation hybrid rice technology (TGHRT) is based on environment-insensitive genic male sterility, which can effectively overcome the intrinsic problems of the three-line and two-line systems. Since the establishment of TGHRT, numerous findings and innovations have been reported. This paper gives a brief review of traditional hybrid rice technologies and discusses the establishment of TGHRT, technical innovations in TGHRT, and future research that is necessary to promote the wide application of TGHRT in rice production.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"4 1","pages":""},"PeriodicalIF":5.5,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138563550","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":"Phosphate Transporter OsPT4, Ubiquitinated by E3 Ligase OsAIRP2, Plays a Crucial Role in Phosphorus and Nitrogen Translocation and Consumption in Germinating Seed.","authors":"Yafei Sun, Fang Zhang, Jia Wei, Ke Song, Lijuan Sun, Yang Yang, Qin Qin, Shiyan Yang, Zhouwen Li, Guohua Xu, Shubin Sun, Yong Xue","doi":"10.1186/s12284-023-00666-9","DOIUrl":"10.1186/s12284-023-00666-9","url":null,"abstract":"<p><p>Phosphorus (P) and nitrogen (N) are essential macronutrients necessary for plant growth and development. OsPT4 is a high-affinity phosphate (Pi) transporter that has a positive impact on nutrient uptake and seed development. In this study, the expression patterns of different Pi transporter genes in germinating seeds were determined, and the relative expression of OsPT4 was induced in Pi-deficient seeds and gradually increased with the passage of germination time. The analysis of P, N, Pi, and amino acid concentrations in germinating seeds of OsPT4 mutants showed that the OsPT4 mutation caused P and N retention and a continuous reduction in multiple amino acid concentrations in germinating seeds. Transcriptome analysis and qRT-PCR results also indicated that the OsPT4 mutation inhibits the expression of genes related to P and N transportation and amino acid synthesis in germinating seeds. In addition, the paraffin section and TUNEL assay of OsPT4 mutant germinating seeds suggests that OsPT4 mutation causes programmed cell death (PCD) delayed in the aleurone layer and inhibition of leaf outgrowth. Moreover, we also found that OsPT4 was ubiquitinated by OsAIRP2, which is a C3HC4-type RING E3 Ub ligase. Our studies illustrate that OsPT4 plays a crucial role in P and N collaborative translocation and consumption in germinating seeds. It also provides a theoretical basis for the molecules and physiological mechanisms of P and N cross-talk under suppressed Pi uptake conditions.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"54"},"PeriodicalIF":4.8,"publicationDate":"2023-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10697913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138488325","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}
RicePub Date : 2023-12-01DOI: 10.1186/s12284-023-00672-x
Shujun Wei, Ryokei Tanaka, Taiji Kawakatsu, S. Teramoto, Nobuhiro Tanaka, Matthew Shenton, Y. Uga, Shiori Yabe
{"title":"Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice","authors":"Shujun Wei, Ryokei Tanaka, Taiji Kawakatsu, S. Teramoto, Nobuhiro Tanaka, Matthew Shenton, Y. Uga, Shiori Yabe","doi":"10.1186/s12284-023-00672-x","DOIUrl":"https://doi.org/10.1186/s12284-023-00672-x","url":null,"abstract":"","PeriodicalId":21408,"journal":{"name":"Rice","volume":" 53","pages":""},"PeriodicalIF":5.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138612460","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":"Comparative Transcriptome Combined with Morphophysiological Analyses Revealed Carotenoid Biosynthesis for Differential Chilling Tolerance in Two Contrasting Rice (Oryza sativa L.) Genotypes.","authors":"Peng Zhang, Xiang Wu, Yulin Chen, Guangmei Ji, Xinling Ma, Yuping Zhang, Jing Xiang, Yaliang Wang, Zhigang Wang, Liangtao Li, Huizhe Chen, Yikai Zhang","doi":"10.1186/s12284-023-00669-6","DOIUrl":"10.1186/s12284-023-00669-6","url":null,"abstract":"<p><p>Early spring cold spells can lead to leaf chlorosis during the rice seedling greening process. However, the physiological and molecular mechanisms underlying the rice greening process under low-temperature conditions remain unknown. In this study, comparative transcriptome and morphophysiological analyses were performed to investigate the mechanisms mediating the responses of the Koshihikari (Kos) and Kasalath (Kas) rice cultivars to chilling stress. According to their growth-related traits, electrolyte leakage, and chlorophyll fluorescence parameters, Kos was more tolerant to low-temperature stress than Kas. Moreover, chloroplast morphology was more normal (e.g., oval) in Kos than in Kas at 17 °C. The comparative transcriptome analysis revealed 610 up-regulated differentially expressed genes that were common to all four comparisons. Furthermore, carotenoid biosynthesis was identified as a critical pathway for the Kos response to chilling stress. The genes in the carotenoid biosynthesis pathway were expressed at higher levels in Kos than in Kas at 17 °C, which was in accordance with the higher leaf carotenoid content in Kos than in Kas. The lycopene β-cyclase and lycopene ε-cyclase activities increased more in Kos than in Kas. Additionally, the increases in the violaxanthin de-epoxidase and carotenoid hydroxylase activities in Kos seedlings resulted in the accumulation of zeaxanthin and lutein and mitigated the effects of chilling stress on chloroplasts. These findings have clarified the molecular mechanisms underlying the chilling tolerance of rice seedlings during the greening process.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"52"},"PeriodicalIF":5.5,"publicationDate":"2023-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10676345/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138441172","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":"Identification of Genomic Regions for Deep-Water Resistance in Rice for Efficient Weed Control with Reduced Herbicide Use.","authors":"Marina Iwasa, Koki Chigira, Tomohiro Nomura, Shunsuke Adachi, Hidenori Asami, Tetsuya Nakamura, Takashi Motobayashi, Taiichiro Ookawa","doi":"10.1186/s12284-023-00671-y","DOIUrl":"10.1186/s12284-023-00671-y","url":null,"abstract":"<p><p>Deep-water (DW) management in rice fields is a promising technique for efficient control of paddy weeds with reduced herbicide use. Maintaining a water depth of 10-20 cm for several weeks can largely suppress the weed growth, though it also inhibits rice growth because the DW management is usually initiated immediately after transplanting. Improving the DW resistance of rice during the initial growth stage is essential to avoid suppressing growth. In this study, we demonstrate a large genetic variation in the above-ground biomass (AGB) after the end of DW management among 165 temperate japonica varieties developed in Japan. Because the AGB closely correlated with plant length (PL) and tiller number (TN) at the early growth stage, we analyzed genomic regions associated with PL and TN by conducting a genome-wide association study. For PL, a major peak was detected on chromosome 3 (qPL3), which includes a gene encoding gibberellin biosynthesis, OsGA20ox1. The rice varieties with increased PL had a higher expression level of OsGA20ox1 as reported previously. For TN, a major peak was detected on chromosome 4 (qTN4), which includes NAL1 gene associated with leaf morphological development and panicle number. Although there was less difference in the expression level of NAL1 between genotypes, our findings suggest that an amino acid substitution in the exon region is responsible for the phenotypic changes. We also found that the rice varieties having alternative alleles of qPL3 and qTN4 showed significantly higher AGB than the varieties with the reference alleles. Our results suggest that OsGA20ox1 and NAL1 are promising genes for improving DW resistance in rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"16 1","pages":"53"},"PeriodicalIF":5.5,"publicationDate":"2023-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10676340/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138441173","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}