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Free-ranging dogs match a human’s preference in a foraging task

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Current Zoology 2024年第3期70卷 343-349页

作者： Giulia Cimarelli Magdelena Juskaite Friederike Range Sarah Marshall-Pescini domestication Lab Konrad Lorenz Institute of EthologyDepartment of Interdisciplinary Life SciencesUniversity of Veterinary Medicine ViennaVeterinärplatz 11210ViennaAustria Department of Biology Education Stockholm UniversityStockholmSweden

Social learning is a mechanism used by many species to effciently gain information about their *** many animals live in an environment where members of other species are present,little is known about interspecifc social *** and urbanized species provide the opportunity to investigate whether nonhuman animals can learn from heterospecifcs such as humans,who are integral parts of their social *** domestic dogs Canis familiaris have been intensively researched for their ability to learn from humans,most studies have focused on dogs living as ***,free-ranging dogs represent the majority of the world’s dog population,they live alongside humans,scavenge on human refuse,and are subject to natural and sexual ***,free-ranging dogs with extensive exposure to humans and their artifacts provide the opportunity to investigate interspecifc social learning in a naturalistic setting,where learning from humans might be a beneft for *** we tested individual free-ranging dogs in a between-subject design:Dogs in the control group could spontaneously choose between two novel and differently patterned food-delivering *** the experimental group,instead,dogs could frst observe an unfamiliar human approaching and eating from 1 of the 2 *** provide the frst evidence that free-ranging dogs match the choice of an unfamiliar *** results show that at least simple forms of interspecifc social learning might be involved in dogs’success in living alongside humans in a complex urbanized environment.

关键词： Canis familiaris dogs domestication foraging free-ranging dogs social learning urbanization.

A pan-TE map highlights transposable elements underlying domestication and agronomic traits in Asian rice

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National Science Review 2024年第6期11卷 105-118页

作者： Xiaoxia Li Xiaofan Dai Huiying He Yang Lv Longbo Yang Wenchuang He Congcong Liu Hua Wei Xiangpei Liu Qiaoling Yuan Xianmeng Wang Tianyi Wang Bintao Zhang Hong Zhang Wu Chen Yue Leng Xiaoman Yu Hongge Qian Bin Zhang Mingliang Guo Zhipeng Zhang Chuanlin Shi Qianqian Zhang Yan Cui Qiang Xu Xinglan Cao Dandan Chen Yongfeng Zhou Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences Rice Research Institute Shenyang Agricultural University Yazhouwan National laboratory State Key laboratory of Rice Biology China National Rice Research Institute National Key laboratory of Tropical Crop Breeding Tropical Crops Genetic Resources InstituteChinese Academy of Tropical Agricultural Sciences

Transposable elements(TEs) are ubiquitous genomic components and hard to study due to being highly repetitive. Here we assembled 232 chromosome-level genomes based on long-read sequencing *** the 232 genomes with 15 existing assemblies, we developed a pan-TE map comprising both cultivated and wild Asian rice. We detected 177 084 high-quality TE variations and inferred their derived state using outgroups. We found TEs were one source of phenotypic variation during rice domestication and differentiation. We identified 1246 genes whose expression variation was associated with TEs but not single-nucleotide polymorphisms(SNPs), such as Os Rboh B, and validated Os Rboh B's relative expression activity using a dual-Luciferase(LUC) reporter assays system. Our pan-TE map allowed us to detect multiple novel loci associated with agronomic traits. Collectively, our findings highlight the contributions of TEs to domestication, differentiation and agronomic traits in rice, and there is massive potential for gene cloning and molecular breeding by the high-quality Asian pan-TE map we generated.

关键词： transposable element super pan-genome pan-TE rice

Shaping polyploid wheat for success:Origins,domestication,and the genetic improvement of agronomic traits

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Journal of Integrative Plant Biology 2022年第2期64卷 536-563页

作者： Jie Liu Yingyin Yao Mingming Xin Huiru Peng Zhongfu Ni Qixin Sun State Key laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis and Utilizationthe Ministry of EducationKey Laboratory of Crop Genetic ImprovementNational Plant Gene Research CentreChina Agricultural UniversityBeijing100193 China

Bread wheat(Triticum aestivum L.,AABBDD,2 n=6 x=42),which accounts for most of the cultivated wheat crop worldwide,is a typical allohexaploid with a genome derived from three diploid wild *** wheat arose and evolved via two sequential allopolyploidization events and was further polished through multiple steps of ***,cultivated allohexaploid bread wheat has numerous advantageous traits,including adaptive plasticity,favorable yield traits,and extended end-use quality,which have enabled its cultivation well beyond the ranges of its tetraploid and diploid progenitors to become a global staple food *** the past decade,rapid advances in wheat genomic research have considerably accelerated our understanding of the bases for the shaping of complex agronomic traits in this polyploid ***,we summarize recent advances in characterizing major genetic factors underlying the origin,evolution,and improvement of polyploid *** end with a brief discussion of the future prospects for the design of gene cloning strategies and modern wheat breeding.

关键词： adaptation bread wheat domestication end-use quality photoperiod response polyploid semi-dwarfing breeding vernalization

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Harnessing Knowledge from Maize and Rice domestication for New Crop Breeding

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Molecular Plant 2021年第1期14卷 9-26页

作者： Qiuyue Chen Weiya Li Lubin Tan Feng Tian State Key laboratory of Plant Physiology and Biochemistry National Maize Improvement CenterKey Laboratory of Biology and Genetic Improvement of Maize(MOA)Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100193China laboratory of Genetics University of Wisconsin-MadisonMadisonWl 53706USA Department of Biochemistry University of Wisconsin-MadisonMadisonWl 53706USA State Key laboratory of Agrobiotechnology National Center for Evaluation of Agricultural Wild Plants(Rice)MOE Laboratory of Crop Heterosis and UtilizationChina Agricultural UniversityBeijing 100193China

Crop domestication has fundamentally altered the course of human history,causing a shift from huntergatherer to agricultural societies and stimulating the rise of modern civilization.A greater understanding of crop domestication would provide a theoretical basis for how we could improve current crops and develop new crops to deal with environmental challenges in a sustainable ***,we provide a comprehensive summary of the similarities and differences in the domestication processes of maize and rice,two major staple food crops that feed the *** propose that maize and rice might have evolved distinct genetic solutions toward *** and rice domestication appears to be associated with distinct regulatory and evolutionary *** domestication tended to select de novo,loss-of-function,coding variation,while maize domestication more frequently favored standing,gain-offunction,regulatory *** the gene network level,distinct genetic paths were used to acquire convergent phenotypes in maize and rice domestication,during which different central genes were utilized,orthologous genes played different evolutionary roles,and unique genes or regulatory modules were acquired for establishing new ***,we discuss how the knowledge gained from past domestication processes,together with emerging technologies,could be exploited to improve modern crop breeding and domesticate new crops to meet increasing human demands.

关键词： maize rice regulatot7 and evolutionary mechanism domestication gene network de novo domestication

Structural variation and parallel evolution of apomixis in citrus during domestication and diversification

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National Science Review 2022年第10期9卷 82-97页

作者： Nan Wang Xietian Song Junli Ye Siqi Zhang Zhen Cao Chenqiao Zhu Jianbing Hu Yin Zhou Yue Huang Shuo Cao Zhongjie Liu Xiaomeng Wu Lijun Chai Wenwu Guo Qiang Xu Brandon S.Gaut Anna M.G.Koltunow Yongfeng Zhou Xiuxin Deng Key laboratory of Horticultural Plant Biology (Ministry of Education) Huazhong Agricultural University Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Department of Ecology and Evolutionary Biology University of California Irvine Queensland Alliance for Agriculture and Food Innovation University of Queensland

Apomixis,or asexual seed formation,is prevalent in Citrinae via a mechanism termed nucellar or adventitious ***,multiple embryos of a maternal genotype form directly from nucellar cells in the ovule and can outcompete the developing zygotic embryo as they utilize the sexually derived endosperm for *** nucellar embryony enables the propagation of clonal plants of maternal genetic constitution,it is also a barrier to effective breeding through *** address the genetics and evolution of apomixis in Citrinae,a chromosome-level genome of the Hongkong kumquat(Fortunella hindsii) was assembled following a genome-wide variation map including structural variants(SVs) based on234 Citrinae *** map revealed that hybrid citrus cultivars shelter genome-wide deleterious mutations and SVs into heterozygous states free from recessive selection,which may explain the capability of nucellar embryony in most cultivars during Citrinae *** reve aled that parallel evolution may explain the repeated origin of apomixis in different genera of *** Fortu nella,we found that apomixis of some varieties originated via *** apomictic Fortunella,the locus associated with apomixis contains the FhRWP gene,encoding an RWP-RK domain-containing protein previously shown to be required for nucellar embryogenesis in *** found the heterozygous SV in the FhRWP and CitRWP promoters from apomictic Citrus and Fortunella,due to either two or three miniature inverted transposon element(MITE) insertions.A transcription factor,FhARID,encoding an AT-rich interaction domain-containing protein binds to the MITEs in the promoter of apomictic varieties,which facilitates induction of nucellar *** study provides evolutionary genomic and molecular insights into apomixis in Citrinae and has potential ramifications for citrus breeding.

关键词： genomics evolution population genetics apomixis

De novo domestication towards new crops

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National Science Review 2021年第4期8卷 40-41页

作者： Xianrong Xie Yao-Guang Liu State Key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources South China Agricultural University Guangdong laboratory for Lingnan Modern Agriculture College of Life Sciences South China Agricultural University

Long-term natural and human selections have domesticated crops from their wild progenitors for millennia, leading to the fixation of a large number of agronomically beneficial alleles and traits in cultivated crops. However, this process has been extremely time-consuming, accompanied with negative consequences, such as genetic erosion,

关键词： scanning tunneling microscopy phenyl-based molecular film electronic correlation electron-vibration coupling Kondo effect

What happened during domestication of wild to cultivated rice

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The Crop Journal 2021年第3期9卷 564-576页

作者： Ran Xu Chuanqing Sun State Key laboratory of Plant Physiology and Biochemistry China Agricultural UniversityBeijing 100193China

domestication of crops is one of the greatest inventions of the human race and has played a vital role in the progress of human *** the genetic mechanisms of crop domestication could shed light on its history and would advance crop *** rice species,which were domesticated from wild rice species,are important food crops *** traits,physiological characteristics,and ecological adaptability of cultivated rice are very different from those characters of wild *** this review,we summarize current knowledge of the genetic mechanisms underlying these differences between wild and cultivated rice and discuss the application of wild rice species in modern breeding.

关键词： Oryza genus Wild rice Cultivated rice domestication

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Natural Variations at TIG1 Encoding a TCP Tran scription Factor Contribute to Plant Architecture domestication in Rice

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Molecular Plant 2019年第8期12卷 1075-1089页

作者： Weifeng Zhang Lubin Tan Hongying Sun Xinhui Zhao Fengxia Liu Hongwei Cai Yongcai Fu Xianyou Sun Ping Gu Zuofeng Zhu Chuanqing Sun State Key laboratory of Plant Physiology and Biochemistry China Agricultural UniversityBeijing 100193China

The modification of plant architecture is a crucial target in rice domestication and modern genetic *** several genes regulating rice plant architecture have been characterized,the molecular mechanisms underlying rice plant architecture domestication remain largely *** we show that the inclined tiller growth in wild rice is controlled by a single dominant gene,TILLER INCLINED GROWTH 1 (T/Gf),which is located on chromosome 8 and encodes a TCP transcriptional ***1 is primarily expressed in the adaxial side of the tiller base,promotes cell elongation,and enlarges the tiller angle in wild *** in the TIG1 promoter of indica cultivars {tig1 allele) resulted in decreased expression of TIG1 in the adaxial side of tiller base and reduced cell length and tiller angle,leading to the transition from inclined tiller growth in wild rice to erect tiller growth during rice ***1 positively regulates the expression of EXP A3,EXPB5,and SAUR39 to promote cell elongation and increase the tiller *** sweep analysis revealed that the tig1 allele was selected in indica cultivars by human *** cloning and characterization of TIG1 supports a new scenario of plant architecture evolution in rice.

关键词： rice plant architecture tiller angle inclined growth domestication

Genome assembly and resequencing analyses provide new insights into the evolution, domestication and ornamental traits of crape myrtle

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Horticulture Research 2023年第9期10卷 39-54页

作者： Yang Zhou Tangchun Zheng Ming Cai Lu Feng Xiufeng Chi Ping Shen Xin Wang Zhiting Wan Cunquan Yuan Man Zhang Yu Han Jia Wang Huitang Pan Tangren Cheng Qixiang Zhang Beijing Key laboratory of Ornamental Plants Germplasm Innovation&Molecular Breeding National Engineering Research Center for FloricultureBeijing Laboratory of Urban and Rural Ecological EnvironmentEngineering Research Center of Landscape Environment of Ministry of EducationKey Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of EducationSchool of Landscape ArchitectureBeijing Forestry UniversityBeijing 100083China

Crape myrtle(Lagerstroemia indica)is a globally used ornamental woody plant and is the representative species of ***,studies on the evolution and genomic breeding of *** have been hindered by the lack of a reference *** we assembled the first high-quality genome of *** using PacBio combined with Hi-C scaffolding to anchor the 329.14-Mb genome assembly into 24 *** detected a previously undescribed independent whole-genome triplication event occurring 35.5 million years ago in *** following its divergence from Punica *** resequencing 73 accessions of Lagerstroemia,the main parents of modern crape myrtle cultivars were found to be *** and *** the process of domestication,genetic diversity tended to decrease in many plants,but this was not observed in *** constructed a high-density genetic linkage map with an average map distance of 0.33 ***,we integrated the results of quantitative trait locus(QTL)using genetic mapping and bulk segregant analysis(BSA),revealing that the major-effect interval controlling internode length(IL)is located on chr1,which contains CDL15,CRG98,and GID1b1 associated with the phytohormone *** of gene expression of the red,purple,and white flower-colour flavonoid pathways revealed that differential expression of multiple genes determined the flower colour of ***,with white flowers having the lowest gene *** addition,BSA of purple-and green-leaved individuals of populations of *** was performed,and the leaf colour loci were mapped to chr12 and *** these intervals,we identified MYB35,NCED,and *** genome assembly provided a foundation for investigating the evolution,population structure,and differentiation of Myrtaceae species and accelerating the molecular breeding of ***.

关键词： breeding evolution flowers