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Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato

Molecular Plant 2024年第2期17卷 277-296页

作者： Mengxiao Yan Ming Li Yunze Wang Xinyi Wang M-Hossein Moeinzadeh Dora G.Quispe-Huamanquispe Weijuan Fan Yijie Fang Yuqin Wang Haozhen Nie Zhangying Wang Aiko Tanaka Bettina Heider Jan F.Kreuze Godelieve Gheysen Hongxia Wang Martin Vingron Ralph Bock Jun Yang Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai 201602China College of Life Sciences Chongqing Normal UniversityChongqing 401331China Biotechnology and Nuclear Technology Research Institute Sichuan Academy of Agricultural SciencesChengdu 610061China College of Life Sciences Shanghai Normal UniversityShanghai 200234China Department of Computational Molecular Biology Max Planck Institute for Molecular GeneticsIhnestraBe 63-7314195 BerlinGermany Department of Biotechnology Ghent University9000 GhentBelgium Guangdong Provincial Key Laboratory of Crops Genetics and Improvement Crop Research InstituteGuangdong Academy of Agricultural SciencesGuangzhou 510640China Graduate School of Bioagricultural Sciences Nagoya UniversityChikusaNagoya 464-8601Japan international Potato Center(CIP) LimaPeru CAS Center for Excellence of Molecular Plant Sciences Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China Max-Planck-Institut fur Molekulare Pflanzenphysiologie Am Muhlenberg 114476 Potsdam-GolmGermany

The hexaploid sweetpotato(lpomoea batatas)is one of the most important root crops ***,its genetic origin remains controversial,and its domestication history remains *** this study,we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of *** diploid progenitor was likely closely related to lpomoea ae-quatoriensis and contributed the B,subgenome,IbT-DNA2,and the lineage 1 type of chloroplast genome to *** tetraploid progenitor of sweetpotato was most likely *** 4x,which donated the B2 subgenome,IbT-DNA1,and the lineage 2 type of chloroplast *** most likely originated from reciprocal crosses between the diploid and tetraploid progenitors,followed by a subsequent whole-genome *** addition,we detected biased gene exchanges between the subgenomes;the rate of B,to B2 subgenome conversions was nearly three times higher than that of B2 to B subgenome *** analyses revealed that genes involved in storage root formation,maintenance of genome stabil-ity,biotic resistance,sugar transport,and potassium uptake were selected during the speciation and domestication of *** study sheds light on the evolution of sweetpotato and paves the way forimprovementofthiscrop.

关键词： sweetpotato origin gene conversion domestication IbT-DNA HPA

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A geranylgeranyl pyrophosphate synthase gene, Ib GGPS, increases carotenoid contents in transgenic sweetpotato

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Journal of Integrative Agriculture 2022年第9期21卷 2538-2546页

作者： LI Rui-jie ZHAI Hong HE Shao-zhen ZHANG Huan ZHAO Ning LIU Qing-chang Key Laboratory of sweetpotato Biology and Biotechnology Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and UtilizationMinistry of Education/College of Agronomy&BiotechnologyChina Agricultural UniversityBeijing 100193P.R.China

Geranylgeranyl pyrophosphate synthase(GGPS) plays an important role in the biosynthesis of carotenoids. In a previous study, the IbGGPS gene was isolated from a sweetpotato, Ipomoea batatas(L.) Lam., line Nongdafu 14 with high carotenoid contents, but its role and underlying mechanisms in carotenoid biosynthesis in sweetpotato were not investigated. In the present study, the IbGGPS gene was introduced into a sweetpotato cv. Lizixiang and the contents of β-carotene, β-cryptoxanthin, zeaxanthin and lutein were significantly increased in the storage roots of the IbGGPSoverexpressing sweetpotato plants. Further analysis showed that IbGGPS gene overexpression systematically upregulated the genes involved in the glycolytic, 2-C-methyl-D-erythritol-4-phosphate(MEP) and carotenoid pathways,which increased the carotenoid contents in the transgenic plants. These results indicate that the IbGGPS gene has the potential for use in improving the carotenoid contents in sweetpotato and other plants.

关键词： sweetpotato Ipomoea batatas(L.)Lam. IbGGPS overexpression carotenoid

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Inhibition of miR397 by STTM technology to increase sweetpotato resistance to SPVD

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Journal of Integrative Agriculture 2022年第10期21卷 2865-2875页

作者： LI Chen LIU Xuan-xuan ABOUELNASR Hesham MOHAMED HAMED Arisha KOU Meng TANG Wei YAN Hui WANG Xin WANG Xiao-xiao ZHANG Yun-gang LIU Ya-ju GAO Run-fei MA Meng LI Qiang Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/sweetpotato Research Institute Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of SweetpotatoMinistry of Agriculture and Rural AffairsXuzhou 221131P.R.China School of Life Science Jiangsu Normal UniversityXuzhou 221116P.R.China Plant Pathology Department Agriculture and Biology Research DivisionNational Research CenterGiza 12622Egypt Department of Horticulture Faculty of AgricultureZagazig UniversityZagazig 44511Egypt

As a critical food crop,sweetpotato(Ipomoea batatas(L.)Lam.)is widely planted all over the world,but it is deeply affected by sweetpotato Virus Disease(SPVD).The present study utilized short tandem target mimic(STTM)technology to effectively up-regulate the expression of laccase(Ib LACs)by successfully inhibiting the expression of mi *** upstream genes in the lignin synthesis pathway were widely up-regulated by feedback regulation,including phenylalanine ammonialyase(PAL),4-coumarate-Co Aligase(4 CL),hydroxycinnamoyl Co A:shikimatetransferase(HTC),caffeicacid O-methyltransferase(COMT),and cinnamyl alcohol dehydrogenase(CAD).Meanwhile,the activities of PAL and LAC increased significantly,finally leading to increased lignin *** deposition in the cell wall increased the physical defence ability of transgenic sweetpotato plants,reduced the accumulation of SPVD transmitted by Bemisia tabaci(Gennadius),and promoted healthy sweetpotato *** results provide new insights for disease resistance breeding and green production of sweetpotato.

关键词： sweetpotato miR397 STTM SPVD lignin content

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Analysis of genetic diversity and population structure in sweetpotato using SSR markers

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Journal of Integrative Agriculture 2023年第11期22卷 3408-3415页

作者： LIU Cheng ZHAO Ning JIANG Zhi-cheng ZHANG Huan ZHAI Hong HE Shao-zhen GAO Shao-pei LIU Qing-chang Key Laboratory of sweetpotato Biology and Biotechnology Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and UtilizationMinistry of Education/College of Agronomy&BiotechnologyChina Agricultural UniversityBeijing 100193P.R.China

sweetpotato, Ipomoea batatas(L.) Lam., is an important food crop worldwide. Large scale evaluation of sweetpotato germplasm for genetic diversity is necessary to determine the genetic relationships between them and effectively use them in the genetic improvement. In this study, the genetic diversity of 617 sweetpotato accessions, including 376landraces and 162 bred varieties from China and 79 introduced varieties from 11 other countries, was assessed using 30 simple sequence repeat(SSR) primer pairs with high polymorphism. Based on the population structure analysis,these sweetpotato accessions were divided into three groups, Group 1, Group 2 and Group 3, which included 228, 136and 253 accessions, respectively. Consistent results were obtained by phylogenic analysis and principal coordinate analysis(PCoA). Of the three groups, Group 2 showed the highest level of genetic diversity and its accessions were mainly distributed in low-latitude regions. The accessions from South China exhibited the highest level of genetic diversity, which supports the hypothesis that Fujian and Guangdong were the first regions where sweetpotato was introduced to China. Analysis of molecular variance(AMOVA) indicated significant genetic differentiations between the different groups, but low levels of genetic differentiation existed between the different origins and accession *** results provide valuable information for the better utilization of these accessions in sweetpotato breeding.

关键词： sweetpotato genetic diversity population structure SsR

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Construction of a high-density SSR genetic linkage map and identification of QTL for storage-root yield and dry-matter content in sweetpotato

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The Crop Journal 2023年第3期11卷 963-967页

作者： Chenxing Zheng Zhicheng Jiang Yusha Meng Jun Yu Xinsun Yang Huan Zhang Ning Zhao Shaozhen He Shaopei Gao Hong Zhai Qingchang Liu Key Laboratory of sweetpotato Biology and Biotechnology Ministry of Agriculture and Rural Affairs/Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis&UtilizationMinistry of EducationCollege of Agronomy&BiotechnologyChina Agricultural UniversityBeijing 100193China Institute of Rural Development Zhejiang Academy of Agricultural SciencesHangzhou 310021ZhejiangChina Institute of Food Crops Hubei Academy of Agricultural SciencesWuhan 430064HubeiChina

sweetpotato(Ipomoea batatas(L.)Lam.)is a widely grown food crop especially in developing *** storage-root yield and dry-matter content has been the main breeding objective of the crop,and DNA marker-assisted breeding is needed for this *** this study,using a mapping population of 500 F1 individuals from a cross between Xushu 18(female)and Xu 781(male),we constructed a highdensity genetic linkage map of sweetpotato using 601 simple-sequence repeat(SSR)primer *** Xushu 18 map contained 90 linkage groups with 5547 SSR markers and spanned 18,263.5 cM,and the Xu 781 map contained 90 linkage groups with 4599 SSR markers and spanned 18,043.7 cM,representing the highest genome coverage yet reported for *** identified 33 QTL for storage-root yield and 16 QTL for dry-matter content,explaining respectively 6.5%–47.5%and 3.2%–18.9%of *** results provide a foundation for fine-mapping and cloning of QTL and for marker-assisted breeding in sweetpotato.

关键词： sweetpotato SSR linkage map QTL Storage-root yield Dry-matter content

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Exploring and exploiting genetics and genomicsfor sweetpotato improvement: Status andperspectives

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Plant Communications 2022年第5期3卷 38-62页

作者： Mengxiao Yan Haozhen Nie Yunze Wang Xinyi Wang Robert Jarret Jiamin Zhao Hongxia Wang Jun Yang Shanghai Key Laboratory of Plant Functional Genomics and Resources Shanghai Chenshan Botanical GardenShanghai 201602China College of Life Sciences Shanghai Normal UniversityShanghai 200234China USDA-ARS/PGRU GriffinGA 30223USA National Key Laboratory of Plant Molecular Genetics CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China

sweetpotato(Ipomoea batatas(L.)Lam.)is one of the most important root crops cultivated *** of its adaptability,high yield potential,and nutritional value,sweetpotato has become an important food crop,particularly in developing *** ensure adequate crop yields to meet increasing demand,it is essential to enhance the tolerance of sweetpotato to environmental stresses and other yield-limiting *** highly heterozygous hexaploid genome of *** complicates genetic studies and limits improvement of sweetpotato through traditional ***,application of next-generation sequencing and high-throughput genotyping and phenotyping technologies to sweetpotato genetics and genomics research has provided new tools and resources for crop *** this review,we discuss the genomics resources that are available for sweetpotato,including the current reference genome,databases,and available bioinformatics *** systematically review the current state of knowledge on the polyploid genetics of sweetpotato,including studies of its origin and germplasm diversity and the associated mapping of important agricultural *** then outline the conventional and molecular breeding approaches that have been applied to ***,we discuss future goals for genetic studies of sweetpotato and crop improvement via breeding in combination with state-of-the-art multi-omics approaches such as genomic selection and gene *** approaches will advance and accelerate genetic improvement of this important root crop and facilitate its sustainable global production.

关键词： sweetpotato polyploid genetics genomics breeding

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Cloning and Characterization of Full Length cDNA of a CC-NBS-LRR Resistance Gene in sweetpotato

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Agricultural Sciences in China 2009年第5期8卷 538-545页

作者： CHEN Guan-shui ZHOU Yi-fei HOU Li-li PAN Da-ren College of Life Science Fujian Agriculture and Forestry University Fuzhou 350002 P.R.China College of Crop Science Fujian Agriculture and Forestry University Fuzhou 350002 P.R. China

Conserved domain such as nucleotide binding site （NBS） was found in several cloned plant disease resistance genes. Based on the NBS domain, resistance gene analogues （RGAs） have been isolated. A full-length cDNA, SPR1 was obtained by rapid amplification of cDNA ends （RACE） method. Sequence analysis indicated that the length of SPR1 was 3 066 bp, including a complete open reading frame of 2 667 bp encoding SPR1 protein of 888 amino acids. Compared with known NBS-LRR genes, it presented relatively high amino acid sequence identity. The polypeptide has a typical structure of nonT1R-NBS-LRR genes, with NB-ARC, CC, and LRR domains. The SPR1-related sequences belonged to multicopy gene family in sweetpotato genome according to the result of Southern blotting. Semi-quantitative RT-PCR analysis showed SPR1 expressed in all tested tissues. The cloning of putative resistance gene from sweetpotato provides a basis for studying the structure and function of sweetpotato disease-resistance relating genes and disease resistant genetic breeding in sweetpotato. The gene has been submitted to the GenBank database, and the accession number is EF428453.

关键词： sweetpotato NBS (nucleotide binding site) LRR (leucine-rich repeat) R gene (resistance gene)

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Molecular diversity and genetic structure of 380 sweetpotato accessions as revealed by SSR markers

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Journal of Integrative Agriculture 2015年第4期14卷 633-641页

作者： YANG Xin-sun SU Wen-jin WANG Lian-jun LEI Jian CHAI Sha-sha LIU Qing-chang Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization Ministry of Education/China Agricultural University Institute of Food Crops Hubei Academy of Agricultural Sciences

sweetpotato, Ipomoea batatas（L.） Lam., is an important food crop widely cultivated in the world. Evaluation of genetic relationships among diverse cultivars and landraces is necessary for efficient exploitation of genetic diversity in the existing germplasm resources. In the present study, a collection of 380 sweetpotato accessions assembled from different agro-climatic zones of China and other countries were genotyped using 30 SSR primer pairs. Model-based structure analysis separated the germplasm into three populations, P1, P2 and P3, containing 228, 133 and 19 accessions, respectively, which was consistent with the results of phylogenic and principal component analysis（PCA）. Analysis of molecular variance（AMOVA） revealed significant genetic differentiation among inferred populations, accounting for 16.47% of the total molecular variance, however, the differences between the regions were not significant, the total variation were due to the differences between the genotypes within the population. Pairwise fixation index（F ST） suggested that populations P1 and P3 had the highest differentiation, while populations P1 and P2 had the lowest differentiation. The diversity among populations was wide, which confirmed the genetic distinction of populations. Through comparing model-based structure and domestication-based classification, it was found that the accessions of population P1 mainly belonged to modern cultivars, and the accessions of populations P2 and P3 basically corresponded to landraces, by which we suggest that modern cultivars maybe had experienced a two-step domestication history. Our results illustrated clear genetic relationships among 380 sweetpotato accessions, exhibiting the potential of accelerating the process of future sweetpotato breeding program by molecular marker based parental selection.

关键词： genetic diversity population structure simple sequence repeat sweetpotato

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Overexpression of SOS Genes Enhanced Salt Tolerance in sweetpotato

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Journal of Integrative Agriculture 2012年第3期11卷 378-386页

作者： GAO Shang YUAN Li ZHAI Hong LIU Cheng-long HE Shao-zhen LIU Qing-chang Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization Ministry of Education/College of Agriculture and BiotechnologyChina

The production of transgenic sweetpotato （*** 18） plants exhibiting enhanced salt tolerance using salt overly sensitive （SOS） genes was achieved through Agrobacterium tumefaciens-mediated *** strain EHA105 harbors a binary vector pCAMBIA3301 with SOS genes （SOS1,SOS2 and SOS3） and bar *** culture was conducted using 0.3 mg L^-1 phosphinothricin （PPT）.A total of 40 plants were produced from the inoculated 170 cell aggregates via somatic *** analysis showed that 37 of the 40 regenerated plants were transgenic *** in vitro assay demonstrated that superoxide dismutase （SOD） and proline were significantly more accumulated and malonaldehyde （MDA） was significantly less accumulated in 21 transgenic plants than in control plants when they were exposed to 86 mmol L^-1 *** tolerance of these 21 plants was further evaluated with Hoagland solution containing 0,51,86,and 120 mmol L^-1 NaCl in the *** results indicated that 6 of them had significantly better growth and rooting ability than the remaining 15 transgenic plants and control *** of SOS genes in the 6 salt-tolerant transgenic plants was demonstrated by RT-PCR *** study provides an alternative approach for improving salt tolerance of sweetpotato.

关键词： Agrobacterium tumefaciens sweetpotato salt tolerance SOS transgenic plant

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Selection of Parents for Breeding Edible Varieties of sweetpotato with High Carotene Content

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Agricultural Sciences in China 2009年第10期8卷 1166-1173页

作者： MA Dai-fu LI Qiang LI Xiu-ying LI Hong-min TANG Zhong-hou HU Ling CAO Qing-he XIE Yi-ping WANGXin sweetpotato Research institute Chinese Academy of Agricultural Sciences~National Sweetpotato Improvement Center Xuzhou 221121P.R. China

sweetpotato varieties with high carotene content have high value for human health. This work aims to improve the breeding efficiency of special varieties with high carotene content by combining molecular markers and agronomic traits to evaluate and screen the parents. The cluster analysis was carried out to identify and screen promising parents by utilizing phenotypic results of the agronomic and characteristic traits, and RAPD and ISSR markers of 15 parents and their offspring by group crossing. Among different parental materials, greater variations were observed in two important traits, the carotene content and the storage root yield. Negative correlation was found between the carotene content and both fresh and dried root yields. The most significant positive correlation was between the carotene content of parents and that of their offspring, with the coefficient of correlation value of 0.7932＊＊. The relationship based on the agronomic characters of the trial materials was not in agreement with the known genealogy, while that based on the molecular marker data showed better result. Each primer amplified 13.8 bands oflSSR markers on average, in which the rate of polymorphic loci was 89.6%. 9.4 bands of RAPD markers were arnplified per primer, in which the rate of polymorphic bands was 74.46%. Large genetic variation of carotene content was found among the parents. For analyzing the genetic diversity of sweetpotato, the molecular marker methods were better than morphological traits; ISSR markers were more efficient than RAPD markers. The combination of molecular markers and agronomic trait analysis may provide valuable theoretic basis for selection of parents to breed new varieties with high carotene content.

关键词： sweetpotato carotene selection of parents RAPD ISSR cluster analysis

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