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Mohd Rodzik FF, Sudirman NA, Teh CK, Ong AL, Heng HY, Yaakop S, Mohd-Assaad N, Ong-Abdullah M, Ata N, Amit S, Saragih B, Appleton DR, Kulaveerasingam H. Development of Nuclear DNA Markers for Applications in Genetic Diversity Study of Oil Palm-Pollinating Weevil Populations. INSECTS 2023; 14:157. [PMID: 36835726 PMCID: PMC9967927 DOI: 10.3390/insects14020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
The oil palm-pollinating weevil (Elaeidobius kamerunicus Faust) was introduced from Cameroon, West Africa, to Malaysia in 1981, and subsequently, to other oil palm-growing countries as well. This study aims to develop a set of robust E. kamerunicus-specific nuclear DNA markers to directly assess the genetic diversity of the weevil populations. A total of 19,148 SNP and 223,200 SSR were discovered from 48 weevils representing three origins (Peninsular Malaysia, Sabah, and Riau) using RAD tag sequencing. Subsequent filtering steps further reduced these to 1000 SNP and 120 SSR. The selected 220 SNP exhibited a polymorphism information content (PIC) of 0.2387 (±0.1280), and 8 SSR had the PIC of 0.5084 (±0.1928). These markers were found to show sufficient polymorphism, making it possible to assign 180 weevils into three major clusters from Ghana, Cameroon, and Southeast Asia (mainly in Malaysia and Indonesia). These DNA markers successfully confirmed the Cameroon origin of the Southeast Asian cluster. However, the presence of null alleles in the SSR markers, due to limited flexibility of the probe design on the short RAD tags, led to an underestimation of heterozygosity within the populations. Hence, the developed SNP markers turned out to be more efficient than the SSR markers in the genetic diversity assessment of the E. kamerunicus populations. The genetic information provides useful insight into developing guidelines for the genetic monitoring and conservation planning of E. kamerunicus.
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Affiliation(s)
- Fairuz Farhana Mohd Rodzik
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Nurshazwani Amalina Sudirman
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Chee-Keng Teh
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
| | - Ai-Ling Ong
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
| | - Huey-Ying Heng
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
| | - Salmah Yaakop
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Norfarhan Mohd-Assaad
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia
| | - Nabeel Ata
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia
| | - Samsudin Amit
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
| | - Burhanuddin Saragih
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
- Minamas Research Centre Pekanbaru, Jalan Baru Bakal, Tualang Timur, Kecamatan Tualang, Kabupaten Siak, Perawang 28772, Provinsi Riau, Indonesia
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Su K, Guo Y, Zhong W, Lin H, Liu Z, Li K, Li Y, Guo X. High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing. PHYTOPATHOLOGY 2021; 111:659-670. [PMID: 33635092 DOI: 10.1094/phyto-12-19-0480-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca 'Zhuosexiang') and white rot-susceptible cultivar (V. vinifera 'Victoria'). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.
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Affiliation(s)
- Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang 110866, People's Republic of China
| | - Weihao Zhong
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Hong Lin
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
| | - Yuanyuan Li
- College of Horticulture Science and Engineering, Shandong Agricultural University, Shandong 271018, People's Republic of China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, People's Republic of China
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang 110866, People's Republic of China
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Borges dos Santos L, Paulo Gomes Viana J, José Biasotto Francischini F, Victoria Fogliata S, L. Joyce A, Pereira de Souza A, Gabriela Murúa M, J. Clough S, Imaculada Zucchi M. A first draft genome of the Sugarcane borer, Diatraea saccharalis. F1000Res 2020. [DOI: 10.12688/f1000research.26614.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The sugarcane borer (Diatraea saccharalis), a widely distributed moth throughout the Americas, is a pest that affects economically important crops such as sugarcane, sorghum, wheat, maize and rice. Given its significant impact on yield reduction, whole-genome information of the species is needed. Here, we report the first draft assembly of the D. saccharalis genome. Methods: The genomic sequences were obtained using the Illumina HiSeq 2500 whole-genome sequencing of a single adult male specimen. We assembled the short-reads using the SPAdes software and predicted protein-coding genes using MAKER. Genome assembly completeness was assessed through BUSCO and the repetitive content by RepeatMasker. Results: The 453 Mb assembled sequences contain 1,445 BUSCO gene orthologs and 1,161 predicted gene models identified based on homology evidence to the domestic silk moth, Bombyx mori. The repeat content composes 41.18% of the genomic sequences which is in the range of other lepidopteran species. Conclusions: Functional annotation reveals that predicted gene models are involved in important cellular mechanisms such as metabolic pathways and protein synthesis. Thus, the data generated in this study expands our knowledge on the genomic characteristics of this devastating pest and provides essential resources for future genetic studies of the species.
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Zhang D, Xia T, Dang S, Fan G, Wang Z. Investigation of Chinese Wolfberry (Lycium spp.) Germplasm by Restriction Site-Associated DNA Sequencing (RAD-seq). Biochem Genet 2018; 56:575-585. [PMID: 29876687 PMCID: PMC6223726 DOI: 10.1007/s10528-018-9861-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 05/04/2018] [Indexed: 01/02/2023]
Abstract
Chinese wolfberry (Lycium spp.) is an important edible and medicinal plant, with a long cultivation history. The genetic relationships among wild Lycium species and landraces have been unclear for a number of reasons, which has hindered the breeding of modern Chinese wolfberry cultivars. In this study, we collected 19 accessions of Chinese wolfberry germplasm, and constructed the genetic relationship based on RAD-seq markers. We obtained 30.32 Gb of clean data, with the average value of each sample being 1.596 Gb. The average mapping rate was 85.7%, and the average coverage depth was 6.76 X. The phylogeny results distinguished all accessions clearly. All the studied landraces shared their most recent common ancestor with L. barbarum, which indicated that L. barbarum may be involved in cultivation of these landraces. The relationship of some landraces, namely the ‘Ningqi’ series, ‘Qingqi-1’ and ‘Mengqi-1,’ has been supported by the phylogeny results, while the triploid wolfberry was shown to be based on a hybrid between ‘Ningqi-1’ and a tetraploid wolfberry. This study uncovered the genetic background of Chinese wolfberry, and developed the foundation for species classification, accession identification and protection, and the production of hybrid cultivars of wolfberry.
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Affiliation(s)
- Defang Zhang
- Qinghai Academy of Agriculture and Forestry, Qinghai University, Xining, 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, 810016, China
| | - Tao Xia
- Qinghai General Health Biotechnology Co., LTD, Xining, 810003, China
| | - Shaofei Dang
- Laboratory of Cell Biology, Research Institute of Forestry, Chinese Academy of Forestry, Xiangshan Road, Beijing, 100091, China
| | - Guanghui Fan
- Qinghai Academy of Agriculture and Forestry, Qinghai University, Xining, 810016, China
| | - Zhanlin Wang
- Qinghai Academy of Agriculture and Forestry, Qinghai University, Xining, 810016, China.
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