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Genetic dissection of the developmental behavior of plant height in rice under different water supply conditions

Journal of Integrative Agriculture 2016年第12期15卷 2688-2702页

作者： WANG Jiang-xu SUN Jian LI Cheng-xin LIU Hua-long WANG Jing-guo ZHAO Hong-wei ZOU De-tang College of Agriculture Northeast Agricultural University

plant height （PH） is one of the most important agronomic traits of rice, as it directly affects the lodging resistance and the high yield potential. Meanwhile, PH is often constrained by water supply over the entire growth period. In this study, a recombinant inbred line （RIL） derived from Xiaobaijingzi and Kongyu 131 strains grown under drought stress and with normal irrigation over 2 yr （2013 and 2014）, respectively （regarded as four environments）, was used to dissect the genetic basis of PH by developmental dynamics QTL analysis combined with QTL^environment interactions. QTLs with net effects excluding the accumulated effects were detected to explore the relationship between genexgene interactions and genexenvironment interactions in specific growth period. A total of 26 additive QTLs （A-QTLs） and 37 epistatic QTLs （E-QTLs） associated with PH were detected by unconditional and conditional mapping over seven growth periods, qPH-2-3, qPH-4-3, qPH-6-1, qPH-7-1, and qPH-12-5 could be detected by both unconditional and conditional analyses, qPH-4-3 and qPH-7-5 were detected in four stages （periods） to be sequentially expressed QTLs controlling PH continuous variation. QTLs with additive effects （A-QTLs） were mostly expressed in the period $3iS2 （the time interval from stages 2 to 3）, and QTLxenvironment interactions performed actively in the first three stages （periods） which could be an important developmental period for rice to undergo external morphogenesis during drought stress. Several QTLs showed high adaptability for drought stress and many QTLs were closely related to the environments such as qPH-3-5, qPH-2-2 and qPH-6-1. 72.5% of the QTLs with a and aa effects detected by conditional analysis were under drought stress, and the PVE of QTLs detected by conditional analysis under drought stress were also much higher than that under normal irrigation. We infer that environments would influence the detection results and sequential expression of genes was highly i

关键词： rice plant height drought stress QTL developmental behavior environment interactions

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***2 regulates plant height by affecting the main inflorescence length and first effective branch height in Brassica napus L.

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The Crop Journal 2024年第4期12卷 1102-1111页

作者： Chengke Pang Jun Yu Liang Zhang Min Tang Hongfang Liu Ying Cai Feng Chen Jiefu Zhang Wei Hua Xiaodong Wang Ming Zheng Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of Agriculture and Rural AffairsWuhan 430062HubeiChina Key Laboratory of Cotton and Rapeseed Ministry of Agriculture and Rural AffairsKey Laboratory of Jiangsu Province for AgrobiologyInstitute of Industrial CropsJiangsu Academy of Agricultural SciencesNanjing 210014JiangsuChina National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070HubeiChina

Rapeseed(Brassica napus L.)is one of the main oil crops in the world,and increasing its yield is of great significance for ensuring the safety of edible ***,improving rapeseed plant architecture is an effective way to increase rapeseed yield with higher planting ***,the regulatory mechanism of rapeseed plant architecture is poorly *** this study,a dwarf rapeseed mutant dwarf08(df08)is obtained by ethyl methane sulfonate(EMS)-*** decrease in plant height of df08 is mainly caused by the reduction in main inflorescence length and first effective branch height and controlled by a single semi-dominant *** hybrid plants(F1)show a semi-dwarf *** map-based cloning and transgenic assay,we confirm that the nonsynonymous single nucleotide variant(SNV)(C to T)in ***2,which is homologous with Arabidopsis(Arabidopsis thaliana)BIN2,is responsible for the dwarfism of ***2 interacts with BnaBZR1/BES1 and involves in brassinosteroids(BRs)signal *** to Leucine substitution in 284(P284L)enhances the protein stability of ***2-D,disrupts BRs signal transduction and affects the expression of genes regulating cell division,leading to dwarfism of *** study provides a new insight for the mechanism of rapeseed plant height regulation and creates an elite germplasm that can be used for genetic improvement of rapeseed architecture.

关键词： Brassica napus plant height Brassinosteroids BIN2

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Integrated genomic and transcriptomic analysis reveals genes associated with plant height of foxtail millet

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The Crop Journal 2023年第2期11卷 593-604页

作者： Mengyuan Zhu Qiang He Mingjie Lyu Tiantian Shi Qian Gao Hui Zhi Huan Wang Guanqing Jia Sha Tang Xiliu Cheng Rui Wanga Andi Xu Haigang Wang Zhijun Qiao Jun Liu Xianmin Diao Ying Gao National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI) Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China Biotechnology Research Institute Chinese Academy of Agricultural Sciences(CAAS)Beijing 100081China Chengdu National Agricultural Science and Technology Center Chengdu 610213SichuanChina Center for Agricultural Genetic Resources Research Shanxi Agricultural UniversityTaiyuan 030031ShanxiChina Institute of Germplasm Resources and Biotechnology Tianjin Academy of Agricultural SciencesTianjin 300112China

Foxtail millet(Setaria italica)is an important C4 model crop;however,due to its high-density planting and high stature,lodging at the filling stage resulted in a serious reduction in yield and ***,it is imperative to identify and deploy the genes controlling foxtail millet plant *** this study,we used a semi-dwarf line 263A and an elite high-stalk breeding variety,Chuang 29 to construct an F2 population to identify dwarf *** performed transcriptome analysis(RNA-seq)using internode tissues sampled at three jointing stages of 263A and Chuang 29,as well as bulk segregant analysis(BSA)on their F2 population.A total of 8918 differentially expressed genes(DEGs)were obtained from RNA-seq analysis,and GO analysis showed that DEGs were enriched in functions such as‘‘gibberellin metabolic process”and‘‘oxidoreductase activity”,which have previously been shown to be associated with plant height.A total 593 mutated genes were screened by BSA-seq *** hundred and seventy-six out of the 593 mutated genes showed differential expression levels between the two parental lines,and seven genes not only showed differential expression in two or three internode tissues but also showed high genomic variation in coding regions,which indicated they play a crucial role in plant height *** them,we found a gibberellin biosynthesis related GA20 oxidase gene(Seita.5G404900),which had a single-base at the third exon,leading to the frameshift mutation at *** amplified polymorphic sequence assay and association analysis proved the single-base in Seita.5G404900 co-segregated with dwarf phenotype in two independent F2 populations planted in entirely different *** together,the candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height,and the molecular marker will be useful for marker-assisted dwarf breeding.

关键词： Foxtail millet plant height Transcriptome analysis Bulk segregant analysis Functional markers Association analysis

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In silico curation of QTL-rich clusters and candidate gene identification for plant height of bread wheat

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The Crop Journal 2023年第5期11卷 1480-1490页

作者： Dengan Xu Chenfei Jia Xinru Lyu Tingzhi Yang Huimin Qin Yalin Wang Qianlin Hao Wenxing Liu Xuehuan Dai Jianbin Zeng Hongsheng Zhang Xianchun Xia Zhonghu He Shuanghe Cao Wujun Ma College of Agronomy Qingdao Agricultural UniversityQingdao 266109ShandongChina National Wheat Improvement Center Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Many genetic loci for wheat plant height(PH) have been reported, and 26 dwarfing genes have been catalogued. To identify major and stable genetic loci for PH, here we thoroughly summarized these functionally or genetic verified dwarfing loci from QTL linkage analysis and genome-wide association study published from 2003 to 2022. A total of 332 QTL, 270 GWAS loci and 83 genes for PH were integrated onto chromosomes according to their locations in the IWGSC RefSeq v2.1 and 65 QTL-rich clusters(QRC) were defined. Candidate genes in each QRC were predicted based on IWGSC Annotation v2.1 and the information on functional validation of homologous genes in other species. A total of 38 candidate genes were predicted for 65 QRC including three GA2ox genes in QRC-4B-IV, QRC-5A-VIII and QRC-6A-II(Rht24) as well as GA 20-oxidase 2(TaSD1-3A) in QRC-3A-IV. These outcomes lay concrete foundations for mapbased cloning of wheat dwarfing genes and application in breeding.

关键词： QTL-rich clusters plant height Semi-dwarfism Reduced height genes Candidate genes

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Coordination of miR319–TaPCF8 with TaSPL14 orchestrates auxin signaling and biosynthesis to regulate plant height in common wheat

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Journal of Integrative plant Biology 2024年第11期66卷 2362-2378页

作者： Pingan Hao Chao Jian Chenyang Hao Shujuan Liu Jian Hou Hongxia Liu Haixia Liu Xueyong Zhang Huixian Zhao Tian Li College of Life Sciences Northwest A&F UniversityYangling 712100China State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Wheat culms,comprising four to six internodes,are critically involved in determining plant height and lodging resistance,essential factors for field performance and regional *** study revealed the regulatory function of miR319 in common wheat plant *** of tae-miR319 through short tandem target mimics(STTM) caused an increased plant height,while overexpression(OE) of tae-miR319 had the opposite *** a miR319-resistant target gene TaPCF8(rTaPCF8),increased plant ***8 acted as a transcription repressor of downstream genes TaIAAs,which interact physically with *** significant differences of indole-3-acetic acid(IAA) contents indicate the involvement of auxin pathway in miR319-mediated plant height ***,we identified two TaPCF8 haplotypes in global wheat ***8-5A-Hap2,as per association and evolution examinations,was subjected to strong substantial selection throughout wheat *** haplotype,associated with shorter plant height,aligns with global breeding ***,in high-yield wheat breeding,we proposed a potential molecular marker for marker-assisted selection(MAS).Our findings offer fresh perspectives into the molecular mechanisms that underlie the miR319–TaPCF8 module's regulation of plant height by orchestrating auxin signaling and biosynthesis in wheat.

关键词： auxin plant height tae-miR319 TaIAAs TaPCF8 TaSPL14 Triticum aestivum

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Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean(Glycine max ***.)

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Journal of Integrative Agriculture 2022年第7期21卷 1903-1912页

作者： LIU Chen TIAN Yu LIU Zhang-xiong GU Yong-zhe ZHANG Bo LI Ying-hui NA Jie QIU Li-juan School of Life Sciences Liaoning Normal UniversityDalian 116081P.R.China National Key Facility for Gene Resources and Genetic Improvement/Key Laboratory of Crop Germplasm Utilization Ministry of Agriculture and Rural Affairs/Institute of Crop SciencesChinese Academy of Agricultural ScienceBeijing 100081P.R.China School of plant and Environmental Sciences Virginia Polytechnic Institute and State UniversityBlacksburgVA 24060USA

With the development of sequencing technology, insertions-deletions(InDels) have been increasingly reported to be involved in the genetic determination of agronomical traits. However, most studies have focused on the identification and application of short-InDels(1–15 bp) for genetic analysis. The objective of this study was to deeply deploy long-InDels(>15 bp) for the genetic analysis of important agronomic traits in soybean. A total of 13 573 polymorphic long-InDels were identified between parents Zhongpin 03-5373(ZP) and Zhonghuang 13(ZH), which were unevenly distributed on 20 chromosomes of soybean, varying from 321 in Chr11 to 1 246 in Chr18. Consistent with the distribution pattern of annotated genes, the average density of long-InDels in arm regions was significantly higher than that in pericentromeric regions at the P=0.01 level. A total of 2 704(19.9% of total) long-InDels were located in genic regions, including 319 large-effect long-InDels, which resulted in truncated or elongated protein sequences. A previously identified QTL(qP H16) underlying plant height was further analyzed, and it was found that 26 out of 35(74.3%) long-InDel markers located in the qPH16 region showed clear polymorphisms between parents ZP and ZH. Seven markers, including three long-InDels and four previously reported SNP markers, were used to genotype 242 recombinant inbred lines derived from ZP×ZH. As a result, the qPH16 locus was narrowed from a 960-kb region to a 477.55-kb region, containing 65 annotated genes. Therefore, these long-InDels are a complementary genetic resource of SNPs and short-InDels for plant height and can facilitate genetic studies and molecular assisted selection breeding in soybean.

关键词： soybean plant height whole genome re-sequencing long-InDels QTL

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Estimating Key Phenological Dates of Multiple Rice Accessions Using Unmanned Aerial Vehicle-Based plant height Dynamics for Breeding

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Rice science 2024年第5期31卷 617-628,I0066-I0070页

作者： HONG Weiyuan LI Ziqiu FENG Xiangqian QIN Jinhua WANG Aidong JIN Shichao WANG Danying CHEN Song State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 311400China College of Computer Science and Technology Zhejiang Sci-Tech UniversityHangzhou 310018China College of Agriculture Yangtze UniversityJingzhou 434025China plant Phenomics Research Centre Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China

Efficient and high-quality estimation of key phenological dates in rice is of great significance in breeding work. plant height(PH) dynamics are valuable for estimating phenological dates. However, research on estimating the key phenological dates of multiple rice accessions based on PH dynamics has been limited. In 2022, field traits were collected using unmanned aerial vehicle(UAV)-based images across 435 plots, including 364 rice varieties. PH, dates of initial heading(IH) and full heading(FH), and panicle initiation(PI), and growth period after transplanting(GPAT) were collected during the rice growth stage. PHs were extracted using a digital surface model(DSM) and fitted using Fourier and logistic models. Machine learning algorithms, including multiple linear regression, random forest(RF), support vector regression, least absolute shrinkage and selection operator, and elastic net regression, were employed to estimate phenological dates. Results indicated that the optimal percentile of the DSM for extracting rice PH was the 95th(R^(2) = 0.934, RMSE = 0.056 m). The Fourier model provided a better fit for PH dynamics compared with the logistic models. Additionally, curve features(CF) and GPAT were significantly associated with PI, IH, and FH. The combination of CF and GPAT outperformed the use of CF alone, with RF demonstrating the best performance among the algorithms. Specifically, the combination of CF extracted from the logistic models, GPAT, and RF yielded the best performance for estimating PI(R^(2) = 0.834, RMSE = 4.344 d), IH(R^(2) = 0.877, RMSE = 2.721 d), and FH(R^(2) = 0.883, RMSE = 2.694 d). Overall, UAV-based rice PH dynamics combined with machine learning effectively estimated the key phenological dates of multiple rice accessions, providing a novel approach for investigating key phenological dates in breeding work.

关键词： phenological date plant height unmanned aerial vehicle machine learning rice breeding

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A transcriptional cascade involving BBX22 and HY5 finely regulates both plant height and fruit pigmentation in citrus

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Journal of Integrative plant Biology 2024年第8期66卷 1752-1768页

作者： Jialing Fu Li Liao Jiajing Jin Zhihao Lu Juan Sun Lizhi Song Yue Huang Shengjun Liu Ding Huang Yuantao Xu Jiaxian He Bin Hu Yiqun Zhu Fangfang Wu Xia Wang Xiuxin Deng Qiang Xu National Key Laboratory for Germplasm Innovation and Utilization of Horticultural Crops College of Horticulture and Forestry SciencesHuazhong Agricultural UniversityWuhan 430070P.R.China Hubei Hongshan Laboratory Wuhan 430070P.R.China Science and Technology Innovation Research Center of Majia Pomelo Shangrao 334000China

Dwarfing is a pivotal agronomic trait affecting both yield and *** species exhibit substantial variation in plant height,among which internode length is a core ***,the molecular mechanism governing internode elongation remains ***,we unveiled that the transcriptional cascade consisting of B-BOX DOMAIN PROTEIN 22(BBX22)and ELONGATED HYPOCOTYL 5(HY5)finely tunes plant height and internode elongation in ***-of-function mutations of BBX22 in an early-flowering citrus(Citrus hindsii“SJG”)promoted internode elongation and reduced pigment accumulation,whereas ectopic expression of BBX22 in SJG,sweet orange(***),pomelo(***)or heterologous expression of BBX22 in tomato(Solanum lycopersicum)significantly decreased internode ***,exogenous application of gibberellin A3(GA3)rescued the shortened internode and dwarf phenotype caused by *** experiments revealed that BBX22 played a dual role in regulation internode elongation and pigmentation in *** the one hand,it directly bound to and activated the expression of HY5,GA metabolism gene(GA2 OXIDASE 8,GA2ox8),carotenoid biosynthesis gene(PHYTOENE SYNTHASE 1,PSY1)and anthocyanin regulatory gene(Ruby1,a MYB DOMAIN PROTEIN).On the other hand,it acted as a cofactor of HY5,enhancing the ability of HY5 to regulate target genes ***,our results reveal the critical role of the transcriptional cascade consisting of BBX22 and HY5 in controlling internode elongation and pigment accumulation in *** the crosstalk regulatory mechanism between internode elongation and fruit pigmentation provides key genes for breeding of novel types with both dwarf and health-beneficial fortification in citrus.

关键词： anthocyanins BBX22 carotenoids citrus HY5 internode elongation plant height

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The miR166 mediated regulatory module controls plant height by regulating gibberellic acid biosynthesis and catabolism in soybean

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Journal of Integrative plant Biology 2022年第5期64卷 995-1006页

作者： Chen Zhao Jingjing Ma Yaohua Zhang Suxin Yang Xianzhong Feng Jun Yan School of Life Sciences East China Normal UniversityShanghai 200241China Key Laboratory of Soybean Molecular Design Breeding Northeast Institute of Geography and AgroecologyThe Chinese Academy of SciencesChangchun 130102China

MicroRNAs(miRNAs)are endogenous small noncoding RNAs that play critical roles in regulating plant growth and ***,we used Short Tandem Target Mimic(STTM)technology to generate soybean(Glycine max(L.)Merr.)miRNA knockdown lines and identify miRNAs that regulate plant height,a key agronomic trait that affects ***166 successfully silenced miR166 in soybean and upregulated the expression of miR166 target genes,such as *** miR166 knockdown lines(GmSTTM166)displayed a reduced plant height ***,GmSTTM166 plants contained lower levels of bioactive gibberellic acid(GA3)than wild-type plants,and application of exogenous GA partially rescued the dwarf phenotype of *** of miR166 altered the expression of genes involved in GA biosynthesis and *** analysis revealed that ATHB14-LIKE directly represses transcription of the GA biosynthesis genes Gm GA1 and Gm GA2,while activating transcription of the GA catabolic gene GIBBERLLIN 2 OXIDASE2(GmGA2ox2).Collectively,these results reveal a pivotal role for miR166 in the genetic control of plant height in soybean,thereby providing invaluable insights for molecular breeding to improve soybean yield.

关键词： miRNA plant development plant height soybean

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GmSTF accumulation mediated by DELLA protein GmRGAs contributes to coordinating light and gibberellin signaling to reduce plant height in soybean

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The Crop Journal 2024年第2期12卷 432-442页

作者： Zhuang Li Qichao Tu Xiangguang Lyu Qican Cheng Ronghuan Ji Chao Qin Jun Liu Bin Liu Hongyu Li Tao Zhao State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

plant height influences plant architecture,lodging resistance,and yield *** is modulated by gibberellic acid(GA)metabolism and *** proteins,acting as central repressors of GA signaling,integrate various environmental and hormonal signals to regulate plant growth and development in *** examined the role of two DELLA proteins,GmRGAa and GmRGAb,in soybean plant height *** of these proteins led to longer internodes and increased plant height,primarily by increasing cell *** functioned under different light conditions,including red,blue,and far-red light,to repress plant *** studies revealed that GmRGAs interacted with the blue light receptor *** with this,GmCRY1b partially regulated plant height via ***,DELLA proteins were found to stabilize the protein GmSTF1/2,a key positive regulator of *** stabilization led to increased transcription of GmGA2ox-7b and subsequent reduction in plant *** study enhances our understanding of DELLA-mediated plant height control,offering Gmrgaab mutants for soybean structure and yield optimization.

关键词： DELLA protein GmRGAs GmSTFs plant height Soybean

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