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Ro N, Lee GA, Ko HC, Oh H, Lee S, Haile M, Lee J. Exploring Disease Resistance in Pepper ( Capsicum spp.) Germplasm Collection Using Fluidigm SNP Genotyping. PLANTS (BASEL, SWITZERLAND) 2024; 13:1344. [PMID: 38794415 PMCID: PMC11125113 DOI: 10.3390/plants13101344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/01/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
This study utilized a diverse Capsicum accessions (5658) sourced from various species and geographical regions, deposited at the National Agrobiodiversity Center, Genebank. We employed 19 SNP markers through a Fluidigm genotyping system and screened these accessions against eight prevalent diseases of pepper. This study revealed accessions resistant to individual diseases as well as those exhibiting resistance to multiple diseases, including bacterial spot, anthracnose, powdery mildew, phytophthora root rot, and potyvirus. The C. chacoense accessions were identified as resistant materials against bacterial spot, anthracnose, powdery mildew, and phytophthora root rot, underscoring the robust natural defense mechanisms inherent in the wild Capsicum species and its potential uses as sources of resistance for breeding. C. baccatum species also demonstrated to be a promising source of resistance to major pepper diseases. Generally, disease-resistant germplasm has been identified from various Capsicum species. Originating from diverse locations such as Argentina, Bolivia, and the United Kingdom, these accessions consistently demonstrated resistance, indicating the widespread prevalence of disease-resistant traits across varied environments. Additionally, we selected ten pepper accessions based on their resistance to multiple diseases, including CMV, Phytophthora root rot, potyviruses, and TSWV, sourced from diverse geographical regions like Hungary, Peru, the United States, and the Netherlands. This comprehensive analysis provides valuable insights into disease resistance in Capsicum, crucial for fostering sustainable agricultural practices and advancing crop improvement through breeding strategies.
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Affiliation(s)
- Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Gi-An Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Ho-Cheol Ko
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Hyeonseok Oh
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Sukyeung Lee
- International Technology Cooperation Center, Rural Development Administration, Jeonju 54875, Republic of Korea;
| | - Mesfin Haile
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea; (N.R.); (G.-A.L.); (H.-C.K.); (H.O.)
| | - Jundae Lee
- Department of Horticulture, College of Agriculture and Life Sciences, Jeonbuk National University, Jeonju 54896, Republic of Korea
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Yadav IS, Singh N, Wu S, Raupp J, Wilson DL, Rawat N, Gill BS, Poland J, Tiwari VK. Exploring genetic diversity of wild and related tetraploid wheat species Triticum turgidum and Triticum timopheevii. J Adv Res 2023; 48:47-60. [PMID: 36084813 PMCID: PMC10248793 DOI: 10.1016/j.jare.2022.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION The domestication bottleneck has reduced genetic diversity inwheat, necessitating the use of wild relatives in breeding programs. Wild tetraploid wheat are widely used in the breeding programs but with morphological characters, it is difficult to distinguish these, resulting in misclassification/mislabeling or duplication of accessions in the Gene bank. OBJECTIVES The study aims to exploreGenotyping by sequencing (GBS) to characterize wild and domesticated tetraploid wheat accessions to generate a core set of accessions to be used in the breeding program. METHODS TASSEL-GBS pipeline was used for SNP discovery, fastStructure was used to determine the population structure and PowerCore was used to generate a core sets. Nucleotide diversity matrices of Nie's and F-statistics (FST) index were used to determine the center of genetic diversity. RESULTS We found 65 % and 47 % duplicated accessions in Triticum timopheevii and T. turgidum respectively. Genome-wide nucleotide diversity and FST scan uncovered a lower intra and higher inter-species differentiation. Distinct FST regions were identified in genomic regions belonging to domestication genes: non-brittle rachis (Btr1) and vernalization (VRN-1).Our results suggest that Israel, Jordan, Syria, and Lebanonas the hub of genetic diversity of wild emmer;Turkey, and Georgia for T. durum; and Iraq, Azerbaijan, and Armenia for theT. timopheevii. Identified core set accessions preserved more than 93 % of the available genetic diversity. Genome wide association study (GWAS) indicated the potential chromosomal segment for resistance to leaf rust in T. timopheevii. CONCLUSION The present study explored the potential of GBS technology in data reduction while maintaining the significant genetic diversity of the species. Wild germplasm showed more differentiation than domesticated accessions, indicating the availability of sufficient diversity for crop improvement. With reduced complexity, the core set preserves the genetic diversity of the gene bank collections and will aid in a more robust characterization of wild germplasm.
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Affiliation(s)
- Inderjit S. Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | | | - Shuangye Wu
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jon Raupp
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Duane L. Wilson
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Bikram S. Gill
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesse Poland
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Vijay K. Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
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Xiao XO, Zhang N, Jin H, Si H. Genetic Analysis of Potato Breeding Collection Using Single-Nucleotide Polymorphism (SNP) Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091895. [PMID: 37176953 PMCID: PMC10181131 DOI: 10.3390/plants12091895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
The autotetraploid potato (Solanum tuberosum L.) is an important crop in China, and it is widely cultivated from Northeast China to South China. Thousands of varieties are bred by breeding institutions or companies, and distinguishing the different varieties based on morphological characteristics is difficult. Using DNA fingerprints is an efficient method to identify varieties that plays an increasingly important role in germplasm identification and property rights protection. In this study, the genetic diversity and population structure of 135 autotetraploid potatoes were evaluated using specific-locus amplified fragment sequencing (SLAF-seq) methods. A total of 3,397,137 high-quality single-nucleotide polymorphisms (SNPs), which were distributed across 12 chromosomes, were obtained. Principal component analysis (PCA), neighbour-joining genetic trees, and model-based structure analysis showed that these autotetraploid potato subpopulations, classified by their SNPs, were not consistent with their geographical origins. On the basis of the obtained 3,397,137 SNPs, 160 perfect SNPs were selected, and 71 SNPs were successfully converted to penta-primer amplification refractory mutation (PARMS-SNP) markers. Additionally, 190 autotetraploid potato varieties were analysed using these 71 PARMS-SNP markers. The PCA results show that the accessions were not completely classified on the basis of their geographical origins. The SNP DNA fingerprints of the 190 autotetraploid potato varieties were also constructed. The SNP fingerprint results show that both synonyms and homonyms were present amongst the 190 autotetraploid potatoes. Above all, these novel SNP markers can lay a good foundation for the analysis of potato genetic diversity, DUS (distinctness, uniformity, and stability) testing, and plant variety protection.
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Affiliation(s)
- Xi-Ou Xiao
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- South Subtropical Crop Research Institution, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Ning Zhang
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Hui Jin
- South Subtropical Crop Research Institution, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang 524091, China
| | - Huaijun Si
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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Genome-wide analysis-based single nucleotide polymorphism marker sets to identify diverse genotypes in cabbage cultivars (Brassica oleracea var. capitata). Sci Rep 2022; 12:20030. [PMID: 36414667 PMCID: PMC9681867 DOI: 10.1038/s41598-022-24477-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 11/16/2022] [Indexed: 11/23/2022] Open
Abstract
Plant variety protection is essential for breeders' rights granted by the International Union for the Protection of New Varieties of Plants. Distinctness, uniformity, and stability (DUS) are necessary for new variety registration; to this end, currently, morphological traits are examined, which is time-consuming and laborious. Molecular markers are more effective, accurate, and stable descriptors of DUS. Advancements in next-generation sequencing technology have facilitated genome-wide identification of single nucleotide polymorphisms. Here, we developed a core set of single nucleotide polymorphism markers to identify cabbage varieties and traits of test guidance through clustering using the Fluidigm assay, a high-throughput genotyping system. Core sets of 87, 24, and 10 markers are selected based on a genome-wide association-based approach. All core markers could identify 94 cabbage varieties and determine 17 DUS traits. A genotypes database was validated using the Fluidigm platform for variety identification, population structure analysis, cabbage breeding, and DUS testing for plant cultivar protection.
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Makombu JG, Cheruiyot EK, Stomeo F, Thuo DN, Oben PM, Oben BO, Zango P, Mialhe E, Ngueguim JR, Mujibi FDN. Species-informative SNP markers for characterising freshwater prawns of genus Macrobrachium in Cameroon. PLoS One 2022; 17:e0263540. [PMID: 36190939 PMCID: PMC9529149 DOI: 10.1371/journal.pone.0263540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 08/16/2022] [Indexed: 11/07/2022] Open
Abstract
Single Nucleotide Polymorphisms (SNPs) are now popular for a myriad of applications in animal and plant species including, ancestry assignment, conservation genetics, breeding, and traceability of animal products. The objective of this study was to develop a customized cost-effective SNP panel for genetic characterisation of Macrobrachium species in Cameroon. The SNPs identified in a previous characterization study were screened as viable candidates for the reduced panel. Starting from a full set of 1,814 SNPs, a total of 72 core SNPs were chosen using conventional approaches: allele frequency differentials, minor allele frequency profiles, and Wright’s Fst statistics. The discriminatory power of reduced set of informative SNPs were then tested using the admixture analysis, principal component analysis, and discriminant analysis of principal components. The panel of prioritised SNP markers (i.e., N = 72 SNPs) distinguished Macrobrachium species with 100% accuracy. However, large sample size is needed to identify more informative SNPs for discriminating genetically closely related species, including M. macrobrachion versus M. vollenhovenii and M. sollaudii versus M. dux. Overall, the findings in this study show that we can accurately characterise Macrobrachium using a small set of core SNPs which could be useful for this economically important species in Cameroon. Given the results obtained in this study, a larger independent validation sample set will be needed to confirm the discriminative capacity of this SNP panel for wider commercial and research applications.
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Affiliation(s)
- Judith G. Makombu
- Department of Fisheries and Aquatic Resources Management, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | | | - Francesca Stomeo
- Biosciences Eastern and Central Africa—International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
| | - David N. Thuo
- Australian National Wildlife Collection, National Research Collections Australia, CSIRO, Canberra, Australia
| | - Pius M. Oben
- Department of Fisheries and Aquatic Resources Management, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | - Benedicta O. Oben
- Department of Fisheries and Aquatic Resources Management, Faculty of Agriculture and Veterinary Medicine, University of Buea, Buea, Cameroon
| | - Paul Zango
- Institute of Fisheries and Aquatic Sciences, University of Douala, Yabassi, Cameroon
| | - Eric Mialhe
- Concepto Azul, Cdlavernaza Norte, Guayaquil, Ecuador
| | - Jules R. Ngueguim
- Institute of Agriculture Research for Development (IRAD), Kribi, Cameroon
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Park JS, Kang MY, Shim EJ, Oh J, Seo KI, Kim KS, Sim SC, Chung SM, Park Y, Lee GP, Lee WS, Kim M, Jung JK. Genome-wide core sets of SNP markers and Fluidigm assays for rapid and effective genotypic identification of Korean cultivars of lettuce ( Lactuca sativa L.). HORTICULTURE RESEARCH 2022; 9:uhac119. [PMID: 35928401 PMCID: PMC9343917 DOI: 10.1093/hr/uhac119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/04/2022] [Indexed: 05/08/2023]
Abstract
Lettuce is one of the economically important leaf vegetables and is cultivated mainly in temperate climate areas. Cultivar identification based on the distinctness, uniformity, and stability (DUS) test is a prerequisite for new cultivar registration. However, DUS testing based on morphological features is time-consuming, labor-intensive, and costly, and can also be influenced by environmental factors. Thus, molecular markers have also been used for the identification of genetic diversity as an effective, accurate, and stable method. Currently, genome-wide single nucleotide polymorphisms (SNPs) using next-generation sequencing technology are commonly applied in genetic research on diverse plant species. This study aimed to establish an effective and high-throughput cultivar identification system for lettuce using core sets of SNP markers developed by genotyping by sequencing (GBS). GBS identified 17 877 high-quality SNPs for 90 commercial lettuce cultivars. Genetic differentiation analyses based on the selected SNPs classified the lettuce cultivars into three main groups. Core sets of 192, 96, 48, and 24 markers were further selected and validated using the Fluidigm platform. Phylogenetic analyses based on all core sets of SNPs successfully discriminated individual cultivars that have been currently recognized. These core sets of SNP markers will support the construction of a DNA database of lettuce that can be useful for cultivar identification and purity testing, as well as DUS testing in the plant variety protection system. Additionally, this work will facilitate genetic research to improve breeding in lettuce.
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Affiliation(s)
- Jee-Soo Park
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Min-Young Kang
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Eun-Jo Shim
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - JongHee Oh
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyoung-In Seo
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames IA 50011, USA
| | - Sung-Chur Sim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Sang-Min Chung
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, South Korea
| | - Gung Pyo Lee
- Department of Plant Science and Technology, Chung-Ang University, Ansung 17546, South Korea
| | - Won-Sik Lee
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Minkyung Kim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
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Wang Y, Wu X, Li Y, Feng Z, Mu Z, Wang J, Wu X, Wang B, Lu Z, Li G. Identification and Validation of a Core Single-Nucleotide Polymorphism Marker Set for Genetic Diversity Assessment, Fingerprinting Identification, and Core Collection Development in Bottle Gourd. FRONTIERS IN PLANT SCIENCE 2021; 12:747940. [PMID: 34868131 PMCID: PMC8636714 DOI: 10.3389/fpls.2021.747940] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Germplasm collections are indispensable resources for the mining of important genes and variety improvement. To preserve and utilize germplasm collections in bottle gourd, we identified and validated a highly informative core single-nucleotide polymorphism (SNP) marker set from 1,100 SNPs. This marker set consisted of 22 uniformly distributed core SNPs with abundant polymorphisms, which were established to have strong representativeness and discriminatory power based on analyses of 206 bottle gourd germplasm collections and a multiparent advanced generation inter-cross (MAGIC) population. The core SNP markers were used to assess genetic diversity and population structure, and to fingerprint important accessions, which could provide an optimized procedure for seed authentication. Furthermore, using the core SNP marker set, we developed an accessible core population of 150 accessions that represents 100% of the genetic variation in bottle gourds. This core population will make an important contribution to the preservation and utilization of bottle gourd germplasm collections, cultivar identification, and marker-assisted breeding.
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Affiliation(s)
- Ying Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaohua Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yanwei Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zishan Feng
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zihan Mu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Jiang Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xinyi Wu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Baogen Wang
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhongfu Lu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guojing Li
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Abstract
The world’s food and agricultural programs have gradually declined into an unsustainable situation due to challenges such as increase in world population, varied agro-climatic regions, increase temperature, extreme sole-culture growing techniques, and water shortage. A considerable emphasis has been put on few staple food crops coupled with repeated dieting, food scarcity, and essential mineral deficits, frequently inducing dietary disorders. Because relying on staple crops may lead to serious food shortages in the future, we must adjust our dietary habits to include a diverse range of non-staple foods and maximize their use in order to achieve food security and reduce the nutritional gap. To assure healthy meals around the world, an authentic and reasonable strategy is presented to draw additional awareness towards variations in agricultural production techniques and dietary preferences. The EAT-Lancet declaration highlighted the importance of increasing agri-based foods to achieve sustainable health. Expanding overlooked crops with abundant genetic stocks and possibly beneficial characteristics is an approach that might meet food and nutritional security challenges. Although undervalued, pumpkin is a valuable vegetable herbaceous plant that contributes to global food and nutritional security. This crop has already been identified as a revolutionary age crop, balanced food, and more adapted to low soil and atmospheric circumstances than other major crops. This review paper focuses on the potential uses of pumpkin as an underutilized crop; diversification and development of hybrids, particularly hybridization breeding through diallel mating design; and how implementation of this “modern” technology would contribute to the breeding of the neglected pumpkin vegetable and stimulate productivity and nourish the world’s largest malnourished, deprived, and starved populations.
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Genome-Wide Association Studies for Striga asiatica Resistance in Tropical Maize. Int J Genomics 2021; 2021:9979146. [PMID: 34239920 PMCID: PMC8238628 DOI: 10.1155/2021/9979146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 11/17/2022] Open
Abstract
Striga asiatica L. is a parasitic weed in cereal crops including maize leading to tremendous yield losses up to 100% under severe infestation. The available S. asiatica control methods include cultural control options such as uprooting and burning the Striga plants before they flower, field sanitation, crop rotation, intercropping, organic matter usage, improved fallows, and application of herbicides. Resource limitation among smallholder farmers renders almost all of the control methods impossible. Development and use of Striga resistant genotypes are seen as the most feasible management option. Marker identification formulates tools that are faster, cheaper, and easier to utilise in breeding for S. asiatica resistance which has low heritability. The objective of this study was to identify single nucleotide polymorphism (SNP) markers for Striga resistance using the genome-wide association study (GWAS). Genotyping by sequencing was done on tropical maize inbred lines followed by their evaluation for Striga resistance. Analysis of variance showed significant (p < 0.05) variation among evaluated genotypes for Striga resistance traits such as germination distance, germination percentage, haustoria root attachments, total Striga plants emerged, total biomass, and growth rate. There were also significant differences (p < 0.05) for cobs, leaves, stems, and roots weight. The broad sense heritability was fairly high (up to 61%) for most traits. The means for derived traits on stress tolerance indices were subjected to a t-test, and significant differences (p < 0.05) were found for leaves, stem, roots, shoots, and total biomass. The Manhattan plots from GWAS showed the presence of three SNP markers on chromosome numbers 5, 6, and 7 for total Striga plants emerged. The identified markers for resistance to S. asiatica should be validated and utilised to breed for Striga resistance in tropical maize.
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Genetic Mapping and Identification of the Candidate Gene for White Seed Coat in Cucurbita maxima. Int J Mol Sci 2021; 22:ijms22062972. [PMID: 33804065 PMCID: PMC8000038 DOI: 10.3390/ijms22062972] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/05/2021] [Accepted: 03/08/2021] [Indexed: 11/16/2022] Open
Abstract
Seed coat color is an important agronomic trait of edible seed pumpkin in Cucurbita maxima. In this study, the development pattern of seed coat was detected in yellow and white seed coat accessions Wuminglv and Agol. Genetic analysis suggested that a single recessive gene white seed coat (wsc) is involved in seed coat color regulation in Cucurbita maxima. An F2 segregating population including 2798 plants was used for fine mapping and a candidate region containing nine genes was identified. Analysis of 54 inbred accessions revealed four main Insertion/Deletion sites in the promoter of CmaCh15G005270 encoding an MYB transcription factor were co-segregated with the phenotype of seed coat color. RNA-seq analysis and qRT-PCR revealed that some genes involved in phenylpropanoid/flavonoid metabolism pathway displayed remarkable distinction in Wuminglv and Agol during the seed coat development. The flanking InDel marker S1548 was developed to predict the seed coat color in the MAS breeding with an accuracy of 100%. The results may provide valuable information for further studies in seed coat color formation and structure development in Cucurbitaceae crops and help the molecular breeding of Cucurbita maxima.
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Discovery of SNP markers of red shrimp Aristeus antennatus for population structure in Western Mediterranean Sea. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01178-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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