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A loss-of-function mutant allele of a glycosyl hydrolase gene has been co-opted for seed weight control during soybean domestication

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Journal of Integrative Plant Biology 2023年第11期65卷 2469-2489页

作者： Siming Wei Bin Yong Hongwei Jiang Zhenghong An Yan Wang Bingbing Li Ce Yang Weiwei Zhu Qingshan Chen Chaoying He State Key Laboratory of Plant Diversity and Specialty Crops/State Key Laboratory of Systematic and Evolutionary Botany Institute of Botanythe Chinese Academy of SciencesBeijing 100093China China National Botanical Garden Beijing 100093China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China College of Agriculture Northeast Agricultural UniversityHarbin 150030China Jilin Academy of Agricultural Sciences Changchun 130022China The Innovative Academy of seed Design the Chinese Academy of SciencesBeijing 100101China

The resultant DNA from loss-of-function mutation can be recruited in biological evolution and ***,we present such a rare and potential case of“to gain by loss”as a neomorphic mutation during soybean domestication for increasing seed *** a population derived from a chromosome segment substitution line of Glycine max(SN14)and Glycine soja(ZYD06),a quantitative trait locus(QTL)of 100-seed weight(q HSW)was mapped on chromosome 11,corresponding to a truncatedβ-1,3-glucosidase(βGlu)*** novel gene hsw results from a 14-bp deletion,causing a frameshift mutation and a premature stop codon in theβ*** contrast to HSW,the hsw completely lostβGlu activity and function but acquired a novel function to promote cell expansion,thus increasing seed *** hsw instead of HSW produced large soybean seeds,and surprisingly,truncating hsw via gene editing further increased the seed *** further found that the core 21-aa peptide of hsw and its variants acted as a promoter of seed *** variation in these transgenic soybean lines substantiated the integration hsw into cell and seed size ***,the hsw allele underwent selection and expansion during soybean domestication and *** work cloned a likely domesticated QTL controlling soybean seed weight,revealed a novel genetic variation and mechanism in soybean domestication,and provided new insight into crop domestication and breeding,and plant evolution.

关键词： domestication frameshift mutation QTL seed weight soybean to gain by loss

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Dt1 inhibits SWEET-mediated sucrose transport to regulate photoperiod-dependent seed weight in soybean

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Molecular Plant 2024年第3期17卷 496-508页

作者： Xiaoming Li Zhonghui Chen Haiyang Li Lin Yue Cuirong Tan Hongjie Liu Yilong Hu Yuhua Yang Xiani Yao Lingping Kong Xiang Huangi Bin Yu Chunyu Zhang Yuefeng Guan Baohui Liu Fanjiang Kong Xingliang Hou Guangdong Provincial Key Laboratory of Applied Botany&State Key Laboratory of Plant Diversity and Specialty Crops South China Botanical GardenChinese Academyof SciencesGuangzhou510650China Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design Guangzhou Key Laboratory of Crop Gene EditingInnovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510006China University of Chinese Academy of Sciences Beijing 100049China College of Agronomy and Biotechnology China Agricultural UniversityBeijing 100193China

Soybean is a photoperiod-sensitive short-day crop whose reproductive period and yield are markedly affected by day-length *** weight is one of the key traits determining the soybean yield;how-ever,the prominent genes that control the final seed weight of soybean and the mechanisms underlying the photoperiod's effect on this trait remain poorly *** this study,we identify SwW19 as a major locus controlling soybean seed weight by QTL mapping and determine Dt1,an orthologous gene of Arabidopsis TFL1 that is known to govern the soybean growth habit,as the causal gene of the SW19 *** showed that Dt1 is highly expressed in developing seeds and regulates photoperiod-dependent seed weight in *** analyses revealed that the Dt1 protein physically interacts with the sucrose transporter GmSWEET10a to negatively regulate the import of sucrose from seed coat to the embryo,thus modulating seed weight under long ***,Dt1 does not function in seed development under short days due to its very low ***,we discovered a novel natural allelic variant of Dt1(H4 haplotype)that decouples its pleiotropic effects on seed size and growth habit;i.e.,this variant remains functional in seed development but fails to regulate the stem growth habit of ***,our findings provide new insights into how soybean seed development responds to photoperiod at different latitudes,offering an ideal genetic component for improving soybean's yield by manipulating its seed weightandgrowth habit.

关键词： soybean seed weight photoperiod dt1 sucrose transport

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Detection of new candidate genes controlling seed weight by integrating gene coexpression analysis and QTL mapping in Brassica napus L.

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The Crop Journal 2023年第3期11卷 842-851页

作者： Hongli Dong Lei Yang Yilin Liu Guifu Tian Huan Tang Shuangshuang Xin Yixin Cui Qing Xiong Huafang Wan Zhi Liu Christian Jung Wei Qian College of Agronomy and Biotechnology Southwest UniversityChongqing 400715China Engineering Research Center of South Upland Agriculture Ministry of EducationChongqing 400715China Department of Hepatobiliary Surgery The Affiliated Drum Tower Hospital of Nanjing University Medical SchoolNanjing 210029JiangsuChina Plant Breeding Institute Christian Albrechts University of KielOlshausenstr.4024098 KielGermany

seed weight is a component of seed yield in rapeseed(Brassica napus L.).Although quantitative trait loci(QTL)for seed weight have been reported in rapeseed,only a few causal quantitative trait genes(QTGs)have been identified,resulting in a limitation in understanding of seed weight *** constructed a gene coexpression network at the early seed developmental stage using transcripts of 20,408 genes in QTL intervals and 1017 rapeseed homologs of known genes from other *** the 10 modules in this gene coexpression network,modules 1 and 2 were core modules and contained genes involved in source–flow–sink processes such as synthesis and transportation of fatty acid and protein,and photosynthesis.A hub gene SERINE CARBOXYPEPTIDASE-LIKE 19(SCPL19)was identified by candidate gene association analysis in rapeseed and functionally investigated using Arabidopsis T-DNA mutant and overexpression *** study demonstrates the power of gene coexpression analysis to prioritize candidate genes from large candidate QTG sets and enhances the understanding of molecular mechanism for seed weight at the early developmental stage in rapeseed.

关键词： Brassica napus L Gene coexpression network Quantitative trait gene SCPL19 seed weight

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Genetic dissection of and genomic selection for seed weight, pod length,and pod width in soybean

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The Crop Journal 2023年第3期11卷 832-841页

作者： Yijie Chen Yajun Xiong Huilong Hong Gang Li Jie Gao Qingyuan Guo Rujian Sun Honglei Ren Fan Zhang Jun Wang Jian Song Lijuan Qiu College of Agriculture Yangtze UniversityJingzhou 434025HubeiChina College of Life Sciences Yangtze UniversityJingzhou 434025HubeiChina National Key Facility for Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China Soybean Research Institute Heilongjiang Academy of Agricultural SciencesHarbin 150086HeilongjiangChina Engineering Research Center of Ecology and Agricultural Use of Wetland Ministry of EducationJingzhou 434025HubeiChina Hulunbuir Institute of Agriculture and Animal Husbandry Hulunbuir 021000Inner MongoliaChina

A biparental soybean population of 364 recombinant inbred lines(RILs)derived from Zhongdou 41×ZYD02.878 was used to identify quantitative trait loci(QTL)associated with hundred-seed weight(100-SW),pod length(PL),and pod width(PW).100-SW,PL,and PW showed moderate correlations among one another,and 100-SW was correlated most strongly with PW(0.64–0.74).Respectively 74,70,75 and19 QTL accounting for 38.7%–78.8%of total phenotypic variance were identified by inclusive composite interval mapping,restricted two-stage multi-locus genome-wide association analysis,3 variancecomponent multi-locus random-SNP-effect mixed linear model analysis,and conditional genome-wide association *** these QTL,189 were novel,and 24 were detected by multiple *** loci were associated with 100-SW,PL,and PW and may be pleiotropic loci.A total of 284 candidate genes were identified in colocalizing QTL regions,including the verified gene seed thickness 1(ST1).Eleven genes with functions involved in pectin biosynthesis,phytohormone,ubiquitin-protein,and photosynthesis pathways were prioritized by examining single nucleotide polymorphism(SNP)variation,calculating genetic differentiation index,and inquiring gene *** prediction accuracies of genomic selection(GS)for 100-SW,PL,and PW based on single trait-associated markers reached 0.82,0.76,and 0.86 respectively,but selection index(SI)-assisted GS strategy did not increase GS efficiency and inclusion of trait-associated markers as fixed effects reduced prediction *** results shed light on the genetic basis of 100-SW,PL,and PW and provide GS models for these traits with potential application in breeding programs.

关键词： Soybean seed weight Pod size Genetic analysis Genomic selection

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BnaUBP15s positively regulates seed size and seed weight in Brassica napus

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Oil Crop Science 2023年第3期8卷 149-155页

作者： Jianwei Gu Jiayin Chen Jie Xia Dengfeng Hong National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan430070China College of Life Science and Technology Hubei Engineering UniversityXiaogan432000China

Brassica napus(***)is a globally significant oilseed crop,making a substantial contribution to both human oil and livestock feed *** seed weight is crucial for improving rapeseed yield;however,only a limited number of seed weight-related genes have been functionally validated in *** thus *** PROTEASE 15(UBP15)belongs to the ubiquitin protease pathway and plays a maternal role in prolonging seed development in *** potential utilization of UBP15 for enhancing seed yield in *** has remained unexplored until *** this study,we identified the orthologs of UBP15 in *** and investigated its functionality using the CRISPR-Cas9 *** generated mutant plants with multiple editing types targeting Bnaubp15s and successfully isolated T-DNA-free homozygous mutant lines that exhibited edits across four homologs of BnaUBP15 in T2 generation *** preliminary data demonstrated that mutation of BnaUBP15s significantly reduced seed size,seed weight,and plant height while noticeably increasing the number of primary *** findings not only provide crucial evidence for further elucidating the molecular mechanism underlying the regulation of seed weight and size by BnaUBP15s but also offer promising novel germplasm for enhancing plant architecture.

关键词： UBP 15 CRISPR-Cas9 seed size seed weight Brassica napus

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seed-Specific Overexpression of Bnrbc S from Oilseed Increases seed weight and Oil Content in Arabidopsis thaliana

Seed-Specific Overexpression of Bnrbc S from Oilseed Increas...

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2010全国植物生物学研讨会

作者： Xue-Long Wu Zhi-Hong Liu Si-Wei Yuan Rui-Zhi Huang Key Laboratory of Plant Metabolic Engineering of Zhejiang Province Institute of Virology and Biotechnology Zhejiang Academy of Agricultural Sciences

Ribulose-1,5-bisphosphate carboxylase/oxygenase(Rubisco),which catalyzes the first step of CO2fixation,is the key photosynthetic enzyme to convert atmospheric carbon to food and support life on the *** higher plants,R... 详细信息

关键词： BnrbcS Brassica napus gene seed weight oil content

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qSWA3-3 encodes a histidine kinase that regulates thousand-seed weight in oilseed rape(Brassica napus L.)

qSWA3-3 encodes a histidine kinase that regulates thousand-s...

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中国作物学会油料作物专业委员会第八次会员代表大会暨学术年会

作者： WANG Hao YAN Min XIN Qiang WAN Li-li YANG Guang-sheng HONG Deng-feng National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University

Thousand-seed weight(TSW) is a major determinant of seed yield in oilseed rape and is a target trait for artificial *** elucidate the genetic mechanism of TWS,we previously prepareda double haploid(DH) population(189 lines) derived from a cross between an elite line ZY50 X and a pol CMS restorer line 7-5 which show significantly difference in seed *** TSW phenotype data of this population was collected from two locations in three years.A genetic linkage map consisting of 2302 SNP markers was constructed based on Alumina 60 K SNP *** mapping with the phenotypic and genotypic data revealed eight TSW QTLs across the *** them,the QTL,qSWA3-3,which explained 8.46-13.70%of the phenotypic variation,could be stably detected in each environment of two *** well understand qSWA3-3,we constructed the BC F near-isogeniclinesin which TSW of NIL(ZY50) was 7.0%higher than that of NIL(7-5),and finally resolved it to a270-kb physical region according to the Darmor-bzh reference *** comparison revealed thata candidate gene encoding a predicted histidine kinase showed obvious differences in both upstream regulation sequence and coding sequence between ZY50 and 7-5,which was then transformed into ZY50 *** the resulting two Tj transgenic families,the transgene-positive plants showed significantly increased TSW compared to the control,suggesting that the histidinekinase-encoding gene was likely to be the causative gene for *** analyses of 505 rapeseed accessions revealed that the accessions carrying the same allele as ZY50 X showed significantly higher TSW than those with other *** study provides novel insights into the molecular mechanisms controlling seed weight and suggests that qSWA3-3 canserve as a potential tool for high-yield breeding of rapeseed.

关键词： Brassica napus seed weight QTL mapping

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seed-Specific Overexpression of BnrbcS from Oilseed Increases seed weight and Oil Content in Arabidopsis thaliana

Seed-Specific Overexpression of BnrbcS from Oilseed Increase...

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植物分子生物学与现代农业——2010全国植物生物学研讨会

作者： Xue-Long Wu,Zhi-Hong Liu,Si-Wei Yuan and Rui-Zhi Huang~* Key Laboratory of Plant Metabolic Engineering of Zhejiang Province,Institute of Virology and Biotechnology,Zhejiang Academy of Agricultural Sciences,310021 Hangzhou,China

Ribulose-1,5-bisphosphate carboxylase/oxygenase(Rubisco),which catalyzes the first step of CO fixation,is the key photosynthetic enzyme to convert atmospheric carbon to food and support life on the *** higher plants,R... 详细信息

关键词： BnrbcS Brassica napus gene seed weight oil content

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*** functions as an important regulator of seed weight in rapeseed(Brassica napus L.)

*** functions as an important regulator of seed weight in ra...

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中国作物学会油料作物专业委员会第八次会员代表大会暨学术年会

作者： ZHANG Xiao-hui YAN Li LI Shi-peng WAN Li-li YANG Guang-sheng HONG Dengfeng National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural University

seed weight(SW) is an important determinant of seed yield potential in Brassicaceae crops and is controlled by naturally occurring quantitative trait locus(QTL).We previously mapped a major QTL,qSW.C9,on chromosome C9 that is colocalized with qSS.C9,a QTL controls the number of seeds per silique(NSS) by using the near-isogenic lines NIL(HZ396) and NIL(Y106) in rapeseed(Brassica napus L.).Our study has shown that the causative gene of qSS.C9,***7 b,specifically regulates NSS but not ***,the other gene from the candidate region will be responsible for the phenotypic variation of *** comparison and transgenic complementation experiment demonstrated that a gene designated ***,much close to ***7 b,can negatively regulate SW in near — isogenic *** pattern analysis showed that *** was expressed in cotyledons,leaves,silique wall,pistils and stamens of *** localization results indicated that *** is localized in *** on the above conclusions,we will further explore the mechanism how *** controls SW and the molecular pathway involved in rapeseed seed *** research will reveal the function of a new gene and help us better understand howthe seed weight is regulated in rapeseed.

关键词： Brassica napus L. QTL seed per silique seed weight

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GmJAZ3 interacts with GmRR18a and GmMYC2a to regulate seed traits in soybean

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Journal of Integrative Plant Biology 2023年第8期65卷 1983-2000页

作者： Yang Hu Yue Liu Jian-Jun Tao Long Lu Zhi-Hao Jiang Jun-Jie Wei Chun-Mei Wu Cui-Cui Yin Wei Li Ying-Dong Bi Yong-Cai Lai Wei Wei Wan-Ke Zhang Shou-Yi Chen Jin-Song Zhang State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China College of Advanced Agricultural Sciences University of Chinese Academy of SciencesBeijing 100049China Key Laboratory of Ministry of Education for Genetics Breeding and Multiple Utilization of CropsCollege of Crop SciencesFujian Agriculture and Forestry UniversityFuzhou 350002China Crop Tillage and Cultivation Institute Heilongjiang Academy of Agricultural SciencesHarbin 150086China Qilu Zhongke Academy of Modern Microbiology Technology Jinan 250000China

seed weight is usually associated with seed size and is one of the important agronomic traits that determine *** of seed weight control is limited,especially in soybean *** we show that Glycine max JASMONATEZIM DOMAIN 3(GmJAZ3),a gene identified through gene co-expression network analysis,regulates seed-related traits in *** of GmJAZ3 promotes seed size/weight and other organ sizes in stable transgenic soybean plants likely by increasing cell ***3 interacted with both *** RESPONSE REGULATOR 18a(GmRR18a)and GmMYC2a to inhibit their transcriptional activation of cytokinin oxidase gene *** CYTOKININ OXIDASE 3-4(GmCKX3-4),which usually affects seed ***,the GmRR18a binds to the promoter of GmMYC2a and activates GmMYC2a gene *** GmJAZ3-overexpressing soybean seeds,the protein contents were increased while the fatty acid contents were reduced compared to those in the control seeds,indicating that the GmJAZ3 affects seed size/weight and *** variation in JAZ3 promoter region was further analyzed and Hap3 promoter correlates with higher promoter activity,higher gene expression and higher seed *** Hap3 promoter may be selected and fixed during soybean ***3 orthologs from other plants/crops may also control seed size and *** together,our study reveals a novel molecular module GmJAZ3-GmRR18a/GmMYC2a-GmCKXs for seed size and weight control,providing promising targets during soybean molecular breeding for better seed traits.

关键词： GmJAz3 response regulator seed size seed weight soybean

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