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Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper(Plectropomus leopardus)

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Zoological Research 2024年第2期45卷 329-340页

作者： Shao-Xuan Wu Qi-Fan Zeng Wen-Tao Han Meng-Ya Wang Hui Ding Ming-Xuan Teng Ming-Yi Wang Pei-Yu Li Xin Gao Zhen-Min Bao Bo Wang Jing-Jie Hu MOE Key Laboratory of Marine Genetics and Breeding College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan ProvinceSanya Oceanographic InstitutionOcean University of ChinaQingdaoShandong/SanyaHainan 266100/572025China Hainan Seed Industry Laboratory SanyaHainan 572025China Southern Marine Science and Engineer Guangdong Laboratory GuangzhouGuangdong 511458China

The leopard coral grouper(Plectropomus leopardus)is a species of significant economic importance.Although artificial cultivation of P.leopardus has thrived in recent decades,the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data.In this study,we identified over 8.73 million single nucleotide polymorphisms(SNPs)through whole-genome resequencing of 326 individuals spanning six distinct groups.Furthermore,we categorized 226 individuals with high-coverage sequencing depth(≥14×)into eight clusters based on their genetic profiles and phylogenetic relationships.Notably,four of these clusters exhibited pronounced genetic differentiation compared with the other populations.To identify potentially advantageous loci for P.leopardus,we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity(θπ)and fixation index(FST)in these four clusters.Using these high-coverage resequencing data,we successfully constructed the first haplotype reference panel specific to P.leopardus.This achievement holds promise for enabling high-quality,cost-effectiveimputationmethods.Additionally,we combined low-coverage sequencing data with imputation techniques for a genome-wide association study,aiming to identify candidate SNP loci and genes associated with growth traits.A significant concentration of these genes was observed on chromosome 17,which is primarily involved in skeletal muscle and embryonic development and cell proliferation.Notably,our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs,showing potential for genetic selective breeding efforts.These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P.leopardus.

关键词： Plectropomus leopardus whole-genome resequencing Growth Haplotype reference panel Single nucleotide polymorphisms

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whole-genome resequencing reveals molecular imprints of anthropogenic and natural selection in wild and domesticated sheep

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Zoological Research 2022年第5期43卷 695-705页

作者： De-Yin Zhang Xiao-Xue Zhang Fa-Di Li Lv-Feng Yuan Xiao-Long Li Yu-Kun Zhang Yuan Zhao Li-Ming Zhao Jiang-Hui Wang Dan Xu Jiang-Bo Cheng Xiao-Bin Yang Wen-Xin Li Chang-Chun Lin Bu-Bo Zhou Wei-Min Wang State Key Laboratory of Grassland Agro-Ecosystems Key Laboratory of Grassland Livestock Industry InnovationMinistry of Agriculture and Rural AffairsEngineering Research Center of Grassland IndustryMinistry of EducationCollege of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhouGansu 730020China College of Animal Science and Technology Gansu Agricultural UniversityLanzhouGansu 730070China Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province MinqinGansu 733300China Lanzhou Veterinary Research Institute Chinese Academy of Agricultural SciencesLanzhouGansu 730046China

The abundance of domesticated sheep varieties and phenotypes is largely the result of long-term natural and artificial selection. However, there is limited information regarding the genetic mechanisms underlying phenotypic variation induced by the domestication and improvement of sheep. In this study, to explore genomic diversity and selective regions at the genome level, we sequenced the genomes of 100 sheep across 10 breeds and combined these results with publicly available genomic data from 225 individuals, including improved breeds, Chinese indigenous breeds,African indigenous breeds, and their Asian mouflon ancestor. Based on population structure, the domesticated sheep formed a monophyletic group,while the Chinese indigenous sheep showed a clear geographical distribution trend. Comparative genomic analysis of domestication identified several selective signatures, including IFI44 and IFI44L genes and PANK2 and RNF24 genes, associated with immune response and visual function.Population genomic analysis of improvement demonstrated that candidate genes of selected regions were mainly associated with pigmentation,energy metabolism, and growth development.Furthermore, the IFI44 and IFI44L genes showed a common selection signature in the genomes of 30domesticated sheep breeds. The IFI44 c. 54413058C>G mutation was selected for genotyping and population genetic validation. Results showed that the IFI44 polymorphism was significantly associated with partial immune traits. Our findings identified the population genetic basis of domesticated sheep at the whole-genome level, providing theoretical insights into the molecular mechanism underlying breed characteristics and phenotypic changes during sheep domestication and improvement.

关键词： Sheep whole-genome resequencing Selection signature analysis Immunity IFI44 gene

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QTL mapping for berry shape based on a high-density genetic map constructed by whole-genome resequencing in grape

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Horticultural Plant Journal 2023年第4期9卷 729-742页

作者： Yandi Wu Yong Wang Xiucai Fan Ying Zhang Jianfu Jiang Lei Sun Qiangwei Luo Feng Sun Chonghuai Liu Zhengzhou Fruit Research Institute Chinese Academy of Agricultural SciencesZhengzhouHenan 450009China Research Institute of Grape and Melon of Xinjiang Uyghur Autonomous Region TurpanXinjiang Uygur Autonomous Region 838200China

Grape berry shape is an important agricultural trait.Clarifying its genetic basis is significant for cultivating grape varieties that meet market demands.However,the current study by forward genetics has not achieved in-depth results.Here,a high-density map was constructed to identify quantitative trait loci(QTLs)for berry shape.A total of 358709 polymorphic SNPs were obtained using whole-genome resequencing(WGS)based on 208 F2 individuals derived from round grape‘E42-6’and oblong grape‘Rizamat’.The 1635.65 cM high-density map was divided into 19 linkage groups with an average distance of 0.37 cM.Using this map,three significant QTLs for fruit shape index(ShI:ratio of berry length to berry width)identified over three years were mapped onto LG4 and LG5,including one stable QTL on Chr5 with the genomic region of 0.47–1.94 Mb.Combining with gene annotation and expression patterns based on RNA-seq data from two contrasting F2 individuals with round and oblong berry(their average ShI was 1.89 and 1.10,respectively)at four developmental stages,four candidate genes were selected from the above QTLs.They were mainly involved in DNA replication,cell wall modification,and phytohormone biosynthesis.Further analysis of RNA-seq data revealed that several important phytohormone synthesis and metabolic pathways were enriched based on differentially expressed genes(DEGs),which was consistent with the results of QTL mapping for genes related to plant hormone biosynthesis in the F2 population.Furthermore,a comparison of plant hormone content showed that there were significant differences in IAA and tZ content between the two contrasting F2 individuals at different developmental stages.Our findings provide molecular insights into the genetic variation in grape berry shape.Stable QTLs and their tightly linked markers offer the possibility of marker-assisted selection to accelerate berry shape breeding.

关键词： Grape Berry shape whole-genome resequencing High-density genetic map QTL

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QTL mapping of quality traits in peanut using whole-genome resequencing

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The Crop Journal 2022年第1期10卷 177-184页

作者： Ziqi Sun Feiyan Qi Hua Liu Li Qin Jing Xu Lei Shi Zhongxin Zhang Lijuan Miao Bingyan Huang Wenzhao Dong Xiao Wang Mengdi Tian Jingjing Feng Ruifang Zhao Xinyou Zhang Zheng Zheng Henan Academy of Crop Molecular Breeding Henan Academy of Agricultural Science/Key Laboratory of Oil Crops in Huang-Huai-Hai PlainsMinistry of Agriculture/Henan Provincial Key Laboratory for Oil Crops ImprovementZhengzhou 450002HenanChina

Oil and protein content and fatty acid composition are quality traits in peanut.Elucidating the genetic mechanisms underlying these traits may help researchers to obtain improved cultivars by molecular breeding.whole-genome resequencing of a recombinant inbred population of 318 lines was performed to construct a high-density linkage map and identify QTL for peanut quality.The map,containing 4561 bin markers,covered 2032 c M with a mean marker density of 0.45 c M.A total of 110 QTL for oil and protein content,and fatty acid composition were mapped on the 18 peanut chromosomes.The QTL q A05.1 was detected in four environments and showed a major phenotypic effect on the contents of oil,protein,and six fatty acids.The genomic region spanned by q A05.1,corresponding to a physical interval of approximately 1.5 Mb,contains two SNPs polymorphic between the parents that could cause missense mutations.The two SNP sites were employed as KASP markers and validated using lines with extremely high and low oil contents.These sites may be useful in the marker-assisted breeding of peanut cultivars with high oil contents.

关键词： QTL mapping Peanut Oil content Fatty acid whole-genome resequencing

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whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass(Micropterus salmoides)

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Zoological Research 2023年第1期44卷 78-89页

作者： Cheng-Fei Sun Xin-Hui Zhang Jun-Jian Dong Xin-Xin You Yuan-Yuan Tian Feng-Ying Gao He-Tong Zhang Qiong Shi Xing Ye Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation Ministry of Agriculture and Rural AffairsPearl River Fisheries Research InstituteChinese Academy of Fishery SciencesGuangzhouGuangdong 510380China Shenzhen Key Lab of Marine Genomics Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic AnimalsBGI Academy of Marine SciencesBGI MarineShenzhenGuangdong 518081China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China

Largemouth bass(Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study,we sequenced 149 largemouth bass fish, including protospecies(imported from the US) and improved breeds(four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection,including several associated with growth(psst1 and grb10), early development(klf9, sp4, and sp8), and immune traits(pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.

关键词： Largemouth bass whole-genome resequencing Signatures of selection Growth Immunity

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whole-genome resequencing of the wheat A subgenome progenitor Triticum urartu provides insights into its demographic history and geographic adaptation

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Plant Communications 2022年第5期3卷 153-170页

作者： Xin Wang Yafei Hu Weiming He Kang Yu Chi Zhang Yiwen Li Wenlong Yang Jiazhu Sun Xin Li Fengya Zheng Shengjun Zhou Lingrang Kong Hongqing Ling Shancen Zhao Dongcheng Liu Aimin Zhang State Key Laboratory of Plant Cell and Chromosome Engineering National Center for Plant Gene ResearchInstitute of Genetics and Developmental Biology/Innovation Academy of Seed DesignChinese Academy of SciencesBeijing 100101China State Key Laboratory of North China Crop Improvement and Regulation College of AgronomyHebei Agricultural UniversityBaoding 071001China Institute of Vegetables Zhejiang Academy of Agricultural SciencesHangzhou 310021China BGI Genomics BGI-ShenzhenShenzhen 518083China State Key Laboratory of Crop Biology Shandong Key Laboratory of Crop BiologyCollege of AgronomyShandong Agricultural UniversityTai’an 271018China BGI Institute of Applied Agriculture BGI-AgroShenzhen 518120China

Triticum urartu is the progenitor of the A subgenome in tetraploid and hexaploid wheat.Uncovering the landscape of genetic variations in T.urartu will help us understand the evolutionary and polyploid characteristics of wheat.Here,we investigated the population genomics of T.urartu by genome-wide sequencing of 59 representative accessions collected around the world.A total of 42.2 million highquality single-nucleotide polymorphisms and 3 million insertions and deletions were obtained by mapping reads to the reference genome.The ancient T.urartu population experienced a significant reduction in effective population size(Ne)from3000000 to140000 and subsequently split into eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations during the Younger Dryas period.A map of allelic drift paths displayed splits and mixtures between different geographic groups,and a strong genetic drift towards hexaploid wheat was also observed,indicating that the direct donor of the A subgenome originated from northwestern Syria.Genetic changes were revealed between the eastern Mediterranean coastal and Mesopotamian-Transcaucasian populations in genes orthologous to those regulating plant development and stress responses.A genome-wide association study identified two single-nucleotide polymorphisms in the exonic regions of the SEMI-DWARF 37 ortholog that corresponded to the different T.urartu ecotype groups.Our study provides novel insights into the origin and genetic legacy of the A subgenome in polyploid wheat and contributes a gene repertoire for genomicsenabled improvements in wheat breeding.

关键词： Triticum urartu whole-genome resequencing demographic history geographic adaptation selective sweep GWAS

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whole-genome sequencing study to identify candidate markers indicating susceptibility to type 2 diabetes in Bama miniature pigs

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动物模型与实验医学(英文) 2023年第4期6卷 283-293页

作者： Miaomiao Niu Yuqiong Zhao Yunxiao Jia Lei Xiang Xin Dai Hua Chen Laboratory Animal Center Chinese PLA General HospitalBeijingPR China Beijing Institute of Orthopaedic Trauma Beijing Jishuitan HospitalBeijingPR China

Background:Hundreds of single-nucleotide polymorphism(SNP)sites have been found to be potential genetic markers of type 2 diabetes mellitus(T2DM).However,SNPs related to T2DM in minipigs have been less reported.This study aimed to screen the T2DM-susceptible candidate SNP loci in Bama minipigs so as to improve the success rate of the minipig T2DM model.Methods:The genomic DNAs of three Bama minipigs with T2DM,six sibling lowsusceptibility minipigs with T2DM,and three normal control minipigs were compared by whole-genome sequencing.The T2DM Bama minipig-specific loci were obtained,and their functions were annotated.Meanwhile,the Biomart software was used to perform homology alignment with T2DM-related loci obtained from the human genome-wide association study to screen candidate SNP markers for T2DM in Bama miniature pigs.Results:whole-genome resequencing detected 6960 specific loci in the minipigs with T2DM,and 13 loci corresponding to 9 diabetes-related genes were selected.Further,a set of 122 specific loci in 69 orthologous genes of human T2DM candidate genes were obtained in the pigs.Collectively,a batch of T2DM-susceptible candidate SNP markers in Bama minipigs,covering 16 genes and 135 loci,was established.Conclusions:whole-genome sequencing and comparative genomics analysis of the orthologous genes in pigs that corresponded to the human T2DM-related variant loci successfully screened out T2DM-susceptible candidate markers in Bama miniature pigs.Using these loci to predict the susceptibility of the pigs before constructing an animal model of T2DM may help to establish an ideal animal model.

关键词： Bama miniature pig candidate marker SNP type 2 diabetes whole-genome resequencing

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Cloning of a candidate resistance gene against Fusarium wilt in sesame using the whole-genome resequencing

Cloning of a candidate resistance gene against Fusarium wilt...

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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...

作者： DUAN Ying-hui MIAO Hong-mei CHANG Shu-xian QU Wen-wen WEI Li-bin LI Chun ZHANG Hai-yang Henan Sesame Research Center Henan Academy of Agricultural Sciences

Sesame Fusarium wilt(SFW),caused by Fusarium oxysporum f.sp.Sesami(FOS),is one of the destructive fungal diseases in sesame,and always threatens the development of sesame production.Improving the resistance of the varieties to SFW disease is urgent and requisite for sesame.Recently,a highly susceptible mutant spl was induced from Yuzhi 11 by EMS mutagenesis.Genetic background analysis proved that the susceptibility phenotype of spl is controlled by single recessive gene(here named SiRS) locus.Subsequently,we performed the genome re-sequencing of the 20 homozygous F plantlets with high resistance and 21 F plantlets with high susceptibility derived from the F populationof the cross spl × Yuzhi 11.A total of 87.2 Gb raw data was obtained by Illumina sequencing platform.Compared with Yuzhi 11 reference genome,183 457 SNPs were found in resistant and susceptible bulk.Association analysis between the two bulks and the SNP-index determined that there were 227 SNPs in an interval of 1.22 Mb on chromosome 3 significantly associated with the mutation trait.Further association analysis found that 2 SNPs in gene SiUTG115363 were identified finally to directly associate with FOS resistance.F population screening proved that the candidate resistance gene SiUTG115363 was co-segregated with phenotype variation.On the other hand,RNA-seq and quantitative real-time PCR analysis showed that the transcripts of SiUTG115363 were induced and accumulated during the FOS infection process.Our results provide a basis for understanding the molecular mechanisms in sesame resistance to FOS.

关键词： sesame Fusarium disease resistance gene gene cloning whole-genome resequencing

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genome-wide scan for selective footprints and genes related to cold tolerance in Chantecler chickens

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Zoological Research 2021年第6期42卷 710-720页

作者： Nai-Yi Xu Wei Si Ming Li Mian Gong Jean-Marc Lariviere Hojjat Asadollahpour Nanaei Pei-Pei Bian Yu Jiang Xin Zhao Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYanglingShaanxi 712100China Department of Animal Science McGill UniversityMontrealQuébec H9X3V9Canada Institut de technologie agroalimentaire du Québec La PocatièreQuébec G0R1Z0Canada

The Chantecler chicken,a unique Canadian indigenous breed,is well adapted to extremely cold environments.However,its genetic characteristics have not been well studied.Here,we analyzed the whole genomes of 10 Chantecler chickens and 121 worldwide chickens,which indicated that Chantecler chickens were derived from commercial chickens and exhibit a high level of inbreeding.Based on a genome-wide scan,we identified two vital candidate regions containing ME3 and ZNF536,which are related to fat metabolism and nervous system in cold adaptation,respectively.We also found that the genetic mechanism of cold adaptation in Chantecler chickens differed from that of chickens from other cold regions,such as northern China.Our study indicated that specialized commercial chickens in the early 20th century contained sufficient genetic diversity to adapt to extreme cold environments over a very short time.These findings enrich our understanding of the adaptive potential of commercial species.

关键词： Chantecler chickens whole-genome resequencing Cold adaptation ME3 ZNF536

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Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys

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Journal of Genetics and Genomics 2021年第8期48卷 737-745页

作者： Jiafei Shen Jie Yu Xuelei Da Mei Li Gang Wang Ningbo Chen Hong Chen Chuzhao Lei Ruihua Dang Key Laboratory of Animal Genetics Breeding and Reproduction of Shaanxi ProvinceCollege of Animal Science and TechnologyNorthwest A&F UniversityYangtingShaanxi 712100China

Donkey(Equus asinus)is an important livestock animal in China because of its draft and medicinal value.After a long period of natural and artificial selection,the variety and phenotype of donkeys have become abundant.We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds.According to population structure,most Chinese domestic donkeys showed a dominant ancestral type.However,the Chinese donkeys still represented a significant geographical distribution trend.In the selective sweep,gene annotation,functional enrichment,and differential expression analyses between large and small donkey groups,we identified selective signals,including NCAPG and LCORL,which are related to rapid growth and large body size.Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.

关键词： Donkey whole-genome resequencing NCAPG LCORL

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