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  • 1
    Online Resource
    Online Resource
    Development of a core set of single nucleotide polymorphism markers for genetic diversity analysis and cultivar fingerprinting in cowpea
    Wiley ; 2021
    In:  Legume Science Vol. 3, No. 3 ( 2021-09)
    Details
    In: Legume Science, Wiley, Vol. 3, No. 3 ( 2021-09)
    Abstract: Cowpea is an important legume crop worldwide. However, the diversity and relationship of current accessions remain unclear due to a lack of robust genetic information. A set of 40,089 single nucleotide polymorphisms (SNPs) adapted to the Kompetitive Allele Specific PCR (KASP) SNP genotyping platform were developed from the existing Illumina Cowpea iSelect Consortium Array for cowpea germplasm genetic diversity assessment and variety identification. Using the genotypic data of 299 cowpea accessions obtained from this SNP assay, a precore pool of 434 SNPs and 50 informative core SNPs was selected and validated for use in future genetic diversity analyses of cowpea germplasm. By further genotyping 75 commercial cultivars using the set of 50 core SNPs, pairwise genotype alignment and dendrogram analysis both showed that each cultivar could be uniquely identified by this core set of markers. The KASP markers developed in this study provide a flexible marker resource for both basic and applied research of cowpea. The precore SNP pool and the core SNP set also provide valuable tools for genetic variation assessment and variety rights protection for cowpea breeders.
    Type of Medium: Online Resource
    ISSN: 2639-6181 , 2639-6181
    URL: Issue
    URL: Article
    DOI: 10.1002/leg3.v3.3
    DOI: 10.1002/leg3.93
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 3009748-4
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  • 2
    Online Resource
    Online Resource
    Long‐read genome assembly and genetic architecture of fruit shape in the bottle gourd
    Wiley ; 2021
    In:  The Plant Journal Vol. 107, No. 3 ( 2021-08), p. 956-968
    Details
    In: The Plant Journal, Wiley, Vol. 107, No. 3 ( 2021-08), p. 956-968
    Abstract: The bottle gourd ( Lagenaria siceraria , Cucurbitaceae) is an important horticultural crop exhibiting tremendous diversity in fruit shape. The genetic architecture of fruit shape variation in this species remains unknown. We assembled a long‐read‐based, high‐quality reference genome (ZAAS_Lsic_2.0) with a contig N50 value over 390‐fold greater than the existing reference genomes. We then focused on dissection of fruit shape using a one‐step geometric morphometrics‐based functional mapping approach. We identified 11 quantitative trait loci (QTLs) responsible for fruit shape (fsQTLs), reconstructed their visible effects and revealed syntenic relationships of bottle gourd fsQTLs with 12 fsQTLs previously reported in cucumber, melon or watermelon. Homologs of several well‐known and newly identified fruit shape genes, including SUN , OFP , AP2 and auxin transporters, were comapped with bottle gourd QTLs.
    Type of Medium: Online Resource
    ISSN: 0960-7412 , 1365-313X
    URL: Issue
    URL: Article
    DOI: 10.1111/tpj.v107.3
    DOI: 10.1111/tpj.15358
    Language: English
    Publisher: Wiley
    Publication Date: 2021
    detail.hit.zdb_id: 2020961-7
    SSG: 12
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  • 3
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    Table_1.xlsx
    Frontiers Media SA ; 2023
    In:  Frontiers in Plant Science Vol. 14 ( 2023-5-12)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 14 ( 2023-5-12)
    Abstract: The snap bean is the most commonly grown vegetable legume worldwide, and its pod size is both an important yield and appearance quality trait. However, the improvement of pod size in snap beans grown in China has been largely hindered by a lack of information on the specific genes that determine pod size. In this study, we identified 88 snap bean accessions and evaluated their pod size traits. Through a genome-wide association study (GWAS), 57 single nucleotide polymorphisms (SNPs) significantly associated with pod size were detected. Candidate gene analysis showed that cytochrome P450 family genes, WRKY, and MYB transcription factors were the predominant candidate genes for pod development, and eight of these 26 candidate genes showed relatively higher expression patterns in flowers and young pods. A significant pod length (PL) SNP and a single pod weight (SPW) SNP were successfully converted into kompetitive allele-specific polymerase chain reaction (KASP) markers and validated in the panel. These results enhance our understanding of the genetic basis of pod size, and also provide genetic resources for the molecular breeding of pod size in snap beans.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2023.1138988
    DOI: 10.3389/fpls.2023.1138988.s001
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2023
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 4
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    Image_4.JPEG
    Frontiers Media SA ; 2021
    In:  Frontiers in Plant Science Vol. 12 ( 2021-5-7)
    Details
    In: Frontiers in Plant Science, Frontiers Media SA, Vol. 12 ( 2021-5-7)
    Abstract: Fusarium wilt (FW) is a typical soil-borne disease that seriously affects the yield and fruit quality of bottle gourd. Thus, to improve resistance to FW in bottle gourd, the genetic mechanism underlying FW resistance needs to be explored. In this study, we performed a genome-wide association study (GWAS) based on 5,330 single-nucleotide polymorphisms (SNPs) and 89 bottle gourd accessions. The GWAS results revealed a total of 10 SNPs ( P ≤ 0.01, −log 10 P ≥ 2.0) significantly associated with FW resistance that were detected in at least two environments (2019DI, 2020DI, and the average across the 2 years); these SNPs were located on chromosomes 1, 2, 3, 4, 8, and 9. Linkage disequilibrium (LD) block structure analysis predicted three potential candidate genes for FW resistance. Genes HG_GLEAN_10001030 and HG_GLEAN_10001042 were within the range of the mean LD block of the marker BGReSe_14202; gene HG_GLEAN_10011803 was 280 kb upstream of the marker BGReSe_00818. Real-time quantitative PCR (qRT-PCR) analysis showed that HG_GLEAN_10011803 was significantly up-regulated in FW-infected plants of YD-4, Yin-10, and Hanbi; HG_GLEAN_10001030 and HG_GLEAN_10001042 were specifically up-regulated in FW-infected plants of YD-4. Therefore, gene HG_GLEAN_10011803 is likely the major effect candidate gene for resistance against FW in bottle gourd. This work provides scientific evidence for the exploration of candidate gene and development of functional markers in FW-resistant bottle gourd breeding programs.
    Type of Medium: Online Resource
    ISSN: 1664-462X
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    URL: Article
    DOI: 10.3389/fpls.2021.650157
    DOI: 10.3389/fpls.2021.650157.s001
    DOI: 10.3389/fpls.2021.650157.s002
    DOI: 10.3389/fpls.2021.650157.s003
    DOI: 10.3389/fpls.2021.650157.s004
    DOI: 10.3389/fpls.2021.650157.s005
    Language: Unknown
    Publisher: Frontiers Media SA
    Publication Date: 2021
    detail.hit.zdb_id: 2687947-5
    detail.hit.zdb_id: 2613694-6
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  • 5
    Online Resource
    Online Resource
    Identification and mapping of a powdery mildew resistance gene Vu-Pm1 in the Chinese asparagus bean landrace ZN016
    Diva Enterprises Private Limited ; 2014
    In:  Legume Research - An International Journal Vol. 37, No. 1 ( 2014), p. 32-
    Details
    In: Legume Research - An International Journal, Diva Enterprises Private Limited, Vol. 37, No. 1 ( 2014), p. 32-
    Type of Medium: Online Resource
    ISSN: 0250-5371 , 0976-0571
    URL: Article
    DOI: 10.5958/j.0976-0571.37.1.005
    Language: English
    Publisher: Diva Enterprises Private Limited
    Publication Date: 2014
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  • 6
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    A universal pipeline for mobile mRNA detection and insights into heterografting advantages under chilling stress
    Oxford University Press (OUP) ; 2020
    In:  Horticulture Research Vol. 7, No. 1 ( 2020-12)
    Details
    In: Horticulture Research, Oxford University Press (OUP), Vol. 7, No. 1 ( 2020-12)
    Abstract: Heterografting has long been used to enhance the chilling tolerance of temperature-sensitive crops, including watermelon, whose mechanism is known to involve bidirectional long-distance mRNA movements. Despite several studies reporting on mobile mRNA (mb-mRNA) profiles in plants, accurate identification of mb-mRNAs is challenging owing to an array of technical problems. Here, we developed a bioinformatical pipeline that took most of the known technical concerns into consideration and is considered to be a universal tool for mb-mRNA detection in heterografts. By applying this pipeline to a commercial watermelon–bottle gourd heterografting system, we detected 130 and 1144 mb-mRNAs upwardly and 167 and 1051 mb-mRNAs downwardly transmitted under normal and chilling-stress conditions, respectively. Quantitative real-time PCR indicated a high accuracy rate (88.2%) of mb-mRNA prediction with our pipeline. We further revealed that the mobility of mRNAs was not associated with their abundance. Functional annotation and classification implied that scions may convey the stress signal to the rootstock, subsequently triggering energy metabolism reprogramming and abscisic acid-mediated stress responses by upward movement of effective mRNAs, ultimately leading to enhanced chilling tolerance. This study provides a universal tool for mb-mRNA detection in plant heterografting systems and novel insights into heterografting advantages under chilling stress.
    Type of Medium: Online Resource
    ISSN: 2662-6810 , 2052-7276
    URL: Article
    DOI: 10.1038/s41438-019-0236-1
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2020
    detail.hit.zdb_id: 2781828-7
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  • 7
    Online Resource
    Online Resource
    Orphan genes are involved in drought adaptations and ecoclimatic-oriented selections in domesticated cowpea
    Oxford University Press (OUP) ; 2019
    In:  Journal of Experimental Botany Vol. 70, No. 12 ( 2019-06-28), p. 3101-3110
    Details
    In: Journal of Experimental Botany, Oxford University Press (OUP), Vol. 70, No. 12 ( 2019-06-28), p. 3101-3110
    Abstract: Orphan genes (OGs) are genes that are restricted to a single species or a particular taxonomic group. To date, little is known about the functions of OGs in domesticated crops. Here, we report our findings on the relationships between OGs and environmental adaptation in cowpea (Vigna unguiculata). We identified 578 expressed OGs, of which 73.2% were predicted to be non-coding. Transcriptomic analyses revealed a high rate of OGs that were drought inducible in roots when compared with conserved genes. Co-expression analysis further revealed the possible involvement of OGs in stress response pathways. Overexpression of UP12_8740, a drought-inducible OG, conferred enhanced tolerance to osmotic stresses and soil drought. By combining Capture-Seq and fluorescence-based Kompetitive allele-specific PCR (KASP), we efficiently genotyped single nucleotide polymorphisms (SNPs) on OGs across a 223 accession cowpea germplasm collection. Population genomic parameters, including polymorphism information content (PIC), expected heterozygosity (He), nucleotide diversity (π), and Tajima’s D statistics, that were calculated based on these SNPs, showed distinct signatures between the grain- and vegetable-type subpopulations of cowpea. This study reinforces the idea that OGs are a valuable resource for identifying new genes related to species-specific environmental adaptations and fosters new insights that artificial selection on OGs might have contributed to balancing the adaptive and agronomic traits in domesticated crops in various ecoclimatic conditions.
    Type of Medium: Online Resource
    ISSN: 0022-0957 , 1460-2431
    URL: Article
    DOI: 10.1093/jxb/erz145
    RVK:
    WA 15000
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2019
    detail.hit.zdb_id: 1466717-4
    SSG: 12
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  • 8
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    Online Resource
    GourdBase: a genome-centered multi-omics database for the bottle gourd (Lagenaria siceraria), an economically important cucurbit crop
    Springer Science and Business Media LLC ; 2018
    In:  Scientific Reports Vol. 8, No. 1 ( 2018-02-26)
    Details
    In: Scientific Reports, Springer Science and Business Media LLC, Vol. 8, No. 1 ( 2018-02-26)
    Abstract: GourdBase is an integrative data platform for the bottle gourd to examine its multifarious intuitive morphology and annotated genome. GourdBase consists of six main modules that store and interlink multi-omic data: the genome (with transcriptomic data integrated) module, the phenome module, the markers/QTLs module, the maps (genetic, physical and comparative) module, the cultivars module, and the publications module. These modules provide access to various type of data including the annotated reference genome sequence, gene models, transcriptomic data from various tissues, physical and comparative genome maps, molecular markers in different types, phenotypic data for featuring traits including fruit shape and umami taste, and quantitative trait loci (QTLs) that underlie these traits. GourdBase is intuitive, user-friendly and interlinked and is designed to allow researchers, breeders and trained farmers to browse, search and fetch information on interests and assist in genomics-driven studies and breeding. The knowledge base and web interface can be accessed at http://www.gourdbase.cn/ .
    Type of Medium: Online Resource
    ISSN: 2045-2322
    URL: Article
    DOI: 10.1038/s41598-018-22007-3
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2018
    detail.hit.zdb_id: 2615211-3
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  • 9
    Online Resource
    Online Resource
    Association Mapping for Fusarium Wilt Resistance in Chinese Asparagus Bean Germplasm
    Wiley ; 2015
    In:  The Plant Genome Vol. 8, No. 2 ( 2015-07)
    Details
    In: The Plant Genome, Wiley, Vol. 8, No. 2 ( 2015-07)
    Abstract: Fusarium wilt (FW) is an important vascular disease attacking asparagus bean [ Vigna unguiculata (L.) Walp. subsp. unguiculata Sesquipedalis Group] in China. The level and genetic variability of FW resistance in the Chinese asparagus bean germplasm remains elusive. In the current study, FW resistance was assessed across a natural population consisting of 95 asparagus bean and four African cowpea [ Vigna unguiculata (L.) Walp. subsp. unguiculata Unguiculata Group] accessions. The disease index (DI) based on the severity of leaf damage (LFD) and vascular discoloration (VD) varied highly across the population and the highly resistant varieties used for vegetable are very limited. Genome‐wide association study identified 11 and seven single nucleotide polymorphisms (SNPs) that are associated with LFD and VD traits, respectively. These SNPs were distributed on nine linkage groups of the asparagus bean genome and each accounted for less than 5% of the phenotypic variation. Overall, the nonstandard vegetable (NSV) subgene pool harbors favorable alleles in a higher frequency than the standard vegetable (SV) subgene pool. Individual NSV‐type accessions tend to possess a greater number of favorable alleles than the SV‐type ones. A SNP marker 1_0981 was converted to a cleaved amplified polymorphic sequences (CAPS) marker to facilitate future breeding. To our knowledge, this is the first report of an association mapping (AM) study in asparagus bean. The results obtained suggests that resources for FW resistance is relatively limited in the SV subgene pool; hence, introducing resistant alleles from the NSV accessions into currently leading SV cultivars will be important to improve FW resistance of the latter.
    Type of Medium: Online Resource
    ISSN: 1940-3372 , 1940-3372
    URL: Article
    DOI: 10.3835/plantgenome2014.11.0082
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 2440458-5
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  • 10
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    SNP marker-based genetic mapping of rust resistance gene in the vegetable cowpea landrace ZN016
    Agricultural Research Communication Center ; 2017
    In:  LEGUME RESEARCH - AN INTERNATIONAL JOURNAL , No. of ( 2017-11-28)
    Details
    In: LEGUME RESEARCH - AN INTERNATIONAL JOURNAL, Agricultural Research Communication Center, , No. of ( 2017-11-28)
    Abstract: Cowpea rust, caused by Uromyces vignae, is one of the most destructive foliar diseases in cowpea [V. unguiculata. (L.) Walp]. Deployment of rust-resistant cultivars is the most environment-friendly and effective way to curb this disease. For this purpose, a fundamental step is to map the rust resistance genes in elite germplasm lines. In the current study, one major and two minor QTLs conferring rust resistance were detected in a 119-line recombinant inbred line (RIL) population derived from a cross between the rust resistant line “ZN016” and a susceptible cultivar “Zhijiang 282”, using the state-of-the-art cowpea iSelect Consortium Array.The major QTL, designated as Ruv1, was mapped to a 12.48 cM interval between the SNP markers 2_01772 and 2_03292 on LG09, which explained 34.8% of the phenotypic variation. The minor QTLs, designated as Ruv2 and Ruv3, were mapped to a 7.01 cM interval on LG7 and a 6.19 cM interval on LG8, which accounted for 13.4% and 11.9% of the phenotypic variation, respectively. This study demonstrates the usefulness of the Consortium SNP Array on complex trait mapping and solidifies the basis for marker-assisted breeding of new cowpea varieties with improved rust resistance.
    Type of Medium: Online Resource
    ISSN: 0976-0571 , 0250-5371
    URL: Article
    DOI: 10.18805/LR-387
    Language: Unknown
    Publisher: Agricultural Research Communication Center
    Publication Date: 2017
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