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breeding melon(Cucumis melo)with resistance to powdery mildew and downy mildew

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Horticultural Plant Journal 2022年第5期8卷 545-561页

作者： Lei Cui Lampros Siskos Chen Wang Henk J.Schouten Richard G.FVisser Yuling Bai College of Agriculture Shanxi Agricultural UniversityTaiyuan030031China Plant breeding Wageningen University&ResearchP.O.Box 3866700 AJWageningenthe Netherlands

Melon(Cucumis melo L.)production is often restricted by a plethora of pests and diseases,including powdery mildew and downy mildew caused respectively by the fungal species Podosphaera xanthii/Golovinomyces orontii and oomycete species Pseudoperonospora cubensis.Many efforts have been directed on identification of resistant sources by screening(wild)melon germplasm.In the current review,we summarized such efforts from various publications of the last 50 plus years.Resistance to powdery mildew has been identified in 239 melon accessions and downy mildew resistance in 452 accessions of both C.melo and the wild relative species C.figarei.Among the resistance sources,C.melo var.cantalupensis accessions PMR 45,PMR 5,PMR 6,and WMR 29 as well as C.melo var.momordica accessions PI 124111,PI 124112,and PI 414723 have been considered as the most valuable germplasm because multiple resistance genes have been identified from these accessions and are widely used in melon resistance breeding.Further genetic mapping in a number of resistant sources has enabled identification of 25 dominant genes,two recessive genes and seven QTLs conferring powdery mildew resistance,as well as eight dominant genes and 11 QTLs for downy mildew resistances.Based on the reported sequences of associated markers,we anchored physically(many of)these genes and QTLs to chromosomes of the melon cv.DHL92 genome.In addition to presenting a comprehensive overview on powdery mildew and downy mildew resistance in(wild)melon germplasm,we suggest strategies aiming at breeding melon with durable and broad-spectrum resistance to pathogens and pests.

关键词： Cucumis melo Melon Powdery mildew Downy mildew Resistance breeding

Pleiotropy Structures Plant Height and Seed Weight Scaling in Barley despite Long History of Domestication and breeding Selection

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Plant Phenomics 2023年第1期5卷 85-93页

作者： Tianhua He Tefera Tolera Angessa Chengdao Li Western Crop Genetics Alliance Agricultural SciencesCollege of ScienceHealthEngineering and EducationMurdoch UniversityMurdochWAAustralia Agriculture and Food Department of Primary Industries and Regional DevelopmentSouth PerthWAAustralia

Size scaling describes the relative growth rates of different body parts of an organism following a positive correlation.Domestication and crop breeding often target the scaling traits in the opposite directions.The genetic mechanism of the size scaling influencing the pattern of size scaling remains unexplored.Here,we revisited a diverse barley(Hordeum vulgare L.)panel with genome-wide single-nucleotide polymorphisms(SNPs)profile and the measurement of their plant height and seed weight to explore the possible genetic mechanisms that may lead to a correlation of the two traits and the influence of domestication and breeding selection on the size scaling.Plant height and seed weight are heritable and remain positively correlated in domesticated barley regardless of growth type and habit.Genomic structural equation modeling systematically evaluated the pleiotropic effect of individual SNP on the plant height and seed weight within a trait correlation network.We discovered seventeen novel SNPs(quantitative trait locus)conferring pleiotropic effect on plant height and seed weight,involving genes with function in diverse traits related to plant growth and development.Linkage disequilibrium decay analysis revealed that a considerable proportion of genetic markers associated with either plant height or seed weight are closely linked in the chromosome.We conclude that pleiotropy and genetic linkage likely form the genetic bases of plant height and seed weight scaling in barley.Our findings contribute to understanding the heritability and genetic basis of size scaling and open a new venue for seeking the underlying mechanism of allometric scaling in plants.

关键词： breeding scaling Plant

A Combined Genomics and Phenomics Approach is Needed to Boost breeding in Sugarcane

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Plant Phenomics 2023年第3期5卷 395-398页

作者： Ting Luo Xiaoyan Liu Prakash Lakshmanan Key Laboratory of Sugarcane Biotechnology and Genetic Improvement(Guangxi) Ministry of Agriculture and Rural AffairsSugarcane Research InstituteGuangxi Academy of Agricultural SciencesGuangxi Key Laboratory of Sugarcane Genetic ImprovementGuangxi Academy of Agricultural SciencesNanning 530007China Interdisciplinary Research Center for Agriculture Green Development in Yangtze River Basin College of Resources and EnvironmentSouthwest UniversityChongqing 400716China Queensland Alliance for Agriculture and Food Innovation University of QueenslandSt Lucia 4067QLDAustralia

Sugarcane is a major food and bioenergy crop globally.It pro-duces~80%of sugar consumed worldwide,with Brazil and India together accounting for 61%of world sugarcane produc-tion in 2021[1].Globally,sugarcane is the 5th largest crop by production value and acreage,and it is also the second largest bioenergy crop[1,2].Modern sugarcane is an interspecific hybrid(Saccharum species hybrid)of wild progenitor species Saccharum officinarum(2n=80;x=10)andSaccharumspon-taneum(2n=40 to 130;x=8)[3].This genetically complex polyploid crop with varied chromosome numbers(100 to 130)has one of the largest genomes(~10 kb)among plants,making sugarcane breeding considerably slow and challenging.

关键词： breeding sugar globally

breeding Effects and Genetic Compositions of a Backbone Parent (Fengbazhan) of Modern indica Rice in China

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Rice science 2022年第5期29卷 397-401,I0001-I0011页

作者： ZHAO Lei ZHOU Shaochuan WANG Chongrong LI Hong HUANG Daoqiang WANG Zhidong ZHOU Degui CHEN Yibo GONG Rong PAN Yangyang Rice Research Institute Guangdong Academy of Agricultural SciencesGuangdong Laboratory for Lingnan Modern AgricultureGuangdong key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering LaboratoryGuangzhou 510640China

Fengbazhan(FBZ)and its derived varieties have been widely cultivated in China,accounting for 22%of China’s paddy fields.Therefore,evaluating the breeding.Effects of FBZ and elucidating its genetic compositions are effective strategies for interpreting the history of modern rice breeding.Using integrative bioinformatics analysis and population validation,we found that the expression of favorable genes on chromosome 6 was important for the breeding of FBZ-derived varieties and these favorable genes were gradually optimized during the breeding process,which was consistent with the conjecture of the‘Rice Core Germplasm breeding Theory’.For several decades,tremendous efforts have been made by Chinese scientists in rice breeding to improve grain yield,nutritional quality and environmental performance,thereby achieving substantial progress in global food security.Several rice breeding technologies have been developed,including semi-dwarf breeding,utilization of heterosis,launching the‘Super Rice Project’,development of green super rice and molecular design breeding(Qian et al,2016;Bai et al,2018;Tang and Cheng,2018;Yu et al,2022).In southern China,rice can be divided into the early,middle and late rice,and the cultivation area in southern China accounts for approximately 80%of China’s rice cultivation area.Currently,several distinct rice varieties are widely cultivated in southern China.

关键词： breeding paddy dwarf

A review of the pangenome:how it affects our understanding of genomic variation,selection and breeding in domestic animals?

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畜牧与生物技术杂志:英文版 2023年第5期14卷 1815-1833页

作者： Ying Gong Yefang Li Xuexue Liu Yuehui Ma Lin Jiang Laboratory of Animal Genetics Breeding and ReproductionMinistry of AgricultureInstitute of Animal SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100193China National Germplasm Center of Domestic Animal Resources Ministry of TechnologyInstitute of Animal SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100193China Centre d’Anthropobiologie et de Génomique de Toulouse UniversitéPaul Sabatier37 allées Jules GuesdeToulouse 31000France

As large-scale genomic studies have progressed,it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level.While domestic animals tend to have complex routes of origin and migration,suggesting a possible omission of some population-specific sequences in the current reference genome.Conversely,the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals(core genome)and is also able to display sequence information unique to each individual(variable genome).The progress of pangenome research in humans,plants and domestic animals has proved that the missing genetic components and the identification of large structural variants(SVs)can be explored through pangenomic studies.Many individual specific sequences have been shown to be related to biological adaptability,phenotype and important economic traits.The maturity of technologies and methods such as third-generation sequencing,Tel-omere-to-telomere genomes,graphic genomes,and reference-free assembly will further promote the development of pangenome.In the future,pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals,providing better insights into animal domestication,evolution and breeding.In this review,we mainly discuss how pangenome analysis reveals genetic variations in domestic animals(sheep,cattle,pigs,chickens)and their impacts on phenotypes and how this can contribute to the understanding of species diversity.Additionally,we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.

关键词： breeding Domestic animals Pangenome Structural variations

Genome-wide signatures of the geographic expansion and breeding of soybean

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Science China(Life Sciences) 2023年第2期66卷 350-365页

作者： Ying-Hui Li Chao Qin Li Wang Chengzhi Jiao Huilong Hong Yu Tian Yanfei Li Guangnan Xing Jun Wang Yongzhe Gu Xingpeng Gao Delin Li Hongyu Li Zhangxiong Liu Xin Jing Beibei Feng Tao Zhao Rongxia Guan Yong Guo Jun Liu Zhe Yan Lijuan Zhang Tianli Ge Xiangkong Li Xiaobo Wang Hongmei Qiu Wanhai Zhang Xiaoyan Luan Yingpeng Han Dezhi Han Ruzhen Chang Yalong Guo Jochen C.Reif Scott A.Jackson Bin Liu Shilin Tian Li-juan Qiu The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)/Key Laboratory of Soybean Biology(Beijing)(MOA) Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Shenzhen Branch Guangdong Laboratory for Lingnan Modern Agriculture/Genome Analysis Laboratory of the Ministry of Agriculture/Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural SciencesShenzhen 518000China Novogene Bioinformatics Institute Beijing 100098China State Key Laboratory of Crop Genetics and Germplasm Enhancement/Cytogenetics Institute Nanjing Agricultural UniversityNanjing 210095China Soybean Research Institute/MOA National Center for Soybean Improvement/MOA Key Laboratory for Biology and Genetic Improvement of Soybean(General)/State Key Laboratory for Crop Genetics and Germplasm Enhancement Nanjing Agricultural UniversityNanjing 210095China College of Agriculture Yangtze UniversityJingzhou 451199China School of Agronomy Anhui Agricultural UniversityHefei 230036China Jilin Academy of Agricultural Sciences Changchun 130119China Hulun Buir Institution of Agricultural Sciences Hulun Buir 021008China Soybean Research Institute Heilongjiang Academy of Agricultural SciencesHarbin 150086China Key Laboratory of Soybean Biology in Chinese Ministry of Education(Key Laboratory of Soybean Biology and breeding/Genetics of Chinese Agriculture Ministry) Northeast Agricultural UniversityHarbin 150030China Heihe Branch of Heilongjiang Academy of Agricultural Sciences Harbin 150086China State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China Department of breeding Research Leibniz Institute of Plant Genetics and Crop Plant Research(IPK)Gatersleben DE D-06466Germany Center for Applied Genetic Technologies University of GeorgiaAthens 30602USA Department of Ecology/Tibetan Centre for Ecology and Conservation at WHU-TU/Hubei Key

Soybean is a leguminous crop that provides oil and protein. Exploring the genomic signatures of soybean evolution is crucial for breeding varieties with improved adaptability to environmental extremes. We analyzed the genome sequences of 2,214 soybeans and proposed a soybean evolutionary route, i.e., the expansion of annual wild soybean(Glycine soja Sieb. & Zucc.) from southern China and its domestication in central China, followed by the expansion and local breeding selection of its landraces(G. max(L.) Merr.). We observed that the genetic introgression in soybean landraces was mostly derived from sympatric rather than allopatric wild populations during the geographic expansion. Soybean expansion and breeding were accompanied by the positive selection of flowering time genes, including GmSPA3c. Our study sheds light on the evolutionary history of soybean and provides valuable genetic resources for its future breeding.

关键词： soybean adaptation introgression flowering time breeding

Genome-wide identification of functional enhancers and their potential roles in pig breeding

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Journal of Animal Science and Biotechnology 2022年第6期13卷 1690-1702页

作者： Yinqiao Wu Yuedong Zhang Hang Liu Yun Gao Yuyan Liu Ling Chen Lu Liu David M.Irwin Chunhui Hou Zhongyin Zhou Yaping Zhang State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunming 650223YunnanChina Kunming College of Life Science University of Chinese Academy of SciencesKunming 650204YunnanChina State Key Laboratory for Conservation and Utilization of Bio-resource in Yunnan Yunnan UniversityKunming 650091YunnanChina School of Life Science Yunnan UniversityKunming 650091YunnanChina Institute of Physical Science and Information Technology Anhui UniversityHefei 230601AnhuiChina Department of Laboratory Medicine and Pathobiology University of TorontoTorontoCanada Department of Biology School of Life SciencesSouthern University of Science and TechnologyShenzhen 518055China Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223YunnanChina

Background:The pig is an economically important livestock species and is a widely applied large animal model in medical research.Enhancers are critical regulatory elements that have fundamental functions in evolution,development and disease.Genome-wide quantification of functional enhancers in the pig is needed.Results:We performed self-transcribing active regulatory region sequencing(STARR-seq)in the porcine kidney epithelial PK15 and testicular ST cell lines,and reliably identified 2576 functional enhancers.Most of these enhancers were located in repetitive sequences and were enriched within silent and lowly expressed genes.Enhancers poorly overlapped with chromatin accessibility regions and were highly enriched in chromatin with the repressive histone modification H3K9me3,which is different from predicted pig enhancers detected using ChIP-seq for H3K27ac or/and H3K4me1 modified histones.This suggests that most pig enhancers identified with STARR-seq are endogenously repressed at the chromatin level and may function during cell type-specific development or at specific developmental stages.Additionally,the PPP3CA gene is associated with the loin muscle area trait and the QKI gene is associated with alkaline phosphatase activity that may be regulated by distal functional enhancers.Conclusions:In summary,we generated the first functional enhancer map in PK15 and ST cells for the pig genome and highlight its potential roles in pig breeding.

关键词： breeding Functional enhancers Pig STARR-seq

Genome-wide selection and introgression of Chinese rice varieties during breeding

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Journal of Genetics and Genomics 2022年第5期49卷 492-501页

作者： Jinyue Ge Junrui Wang Hongbo Pang Fei Li Danjing Lou Weiya Fan Ziran Liu Jiaqi Li Danting Li Baoxuan Nong Zongqiong Zhang Yanyan Wang Jingfen Huang Meng Xing Yamin Nie Xiaorong Xiao Fan Zhang Wensheng Wang Jianlong Xu Sung Ryul Kim Ajay Kohli Guoyou Ye Weihua Qiao Qingwen Yang Xiaoming Zheng National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Guangxi Key Laboratory for Polysaccharide Materials and Modifications School of Marine Sciences and BiotechnologyGuangxi University for NationalitiesNanningJiangsu 530006China College of Life Science Shenyang Normal UniversityShenyangJilin 110034China Liaoning Institute of Pomology YingkouLiaoning 115009China Rice Research Institute Guangxi Academy of Agricultural ScienceNanningGuangxi 530007China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanyaHainan 572000China International Rice Research Institute DAPO box 7777MetroManilaPhilippines Crop Biotech Institute&Department of Genetic Engineering Kyung Hee UniversityYongin 446-701Republic of Korea

China is the largest rice-producing country,but the genomic landscape of rice diversity has not yet been clarified.In this study,we re-sequence 1070 rice varieties collected from China(400)and other regions in Asia(670).Among the six major rice groups(aus,indica-I,indica-II,aromatic,temperate japonica,and tropical japonica),almost all Chinese varieties belong to the indica-II or temperate japonica group.Most Chinese indica varieties belong to indica-II,which consists of two subgroups developed during different phases of rice breeding.The genomic segments underlying the differences between these subgroups span36.32 Mb.The Chinese japonica rice varieties fall into the temperate japonica group,consisting of two subgroups based on their geographical distribution.The genomic segments underlying the differences between these subgroups span 27.69 Mb.These differentiated segments in the Chinese indica varieties span 45 genes with nonsynonymous mutations that are closely related to variations in plant height and grain width.Fifty-four genes with nonsynonymous mutations are associated with the differences in heading date between the two Chinese japonica subgroups.These findings provide new insights into rice diversity in China that will facilitate the molecular breeding.

关键词： Rice Genome selection Introgression Agronomic traits breeding

Smart breeding Platform:A web-based tool for high-throughput population genetics,phenomics,and genomic selection

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Molecular Plant 2024年第5期17卷 677-681页

作者： Huihui Li Xin Li Peng Zhang Yingwei Feng Junri Mi Shang Gao Lele Sheng Mohsin Ali Zikun Yang Liang Li Wei Fang Wensheng Wang Qian Qian Fei Gu Wenbin Zhou State Key Laboratory of Crop Gene Resources and breeding Institute of Crop SciencesChinese Academy of Agricultural Sciences(CAAS)Beijing 100081China Nanfan Research Institute CAASSanyaHainan 572024China DAMO Academy Alibaba GroupHangzhou 310023China Hupan Lab Hangzhou 310023China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhouZhejiang 310006China

Dear Editor,In the era of big data and artificial intelligence,"smart breeding"has become a broad conceptual framework encompassing the paradigm shift of crop breeding to relying on analysis of high-throughput population genetics and phenomics data to conduct genomic selection,allowing identification and optimal use of the genetic potential in crop species(Xiao et al.,2022;Xu et al.,2022;Wang et al.,2023).Most existing tools for analyzing high-throughput breeding data require extensive computational power,complex installation processes,and command-line expertise and are therefore challenging and inconvenient for the majority of researchers and breeders(Brandies and Hogg,2021).

关键词： breeding artificial breed