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Hajibarat Z, Saidi A, Zeinalabedini M, Mousapour Gorji A, Ghaffari MR, Shariati V, Ahmadvand R. Genotyping-by-sequencing and weighted gene co-expression network analysis of genes responsive against Potato virus Y in commercial potato cultivars. PLoS One 2024; 19:e0303783. [PMID: 38787845 PMCID: PMC11125566 DOI: 10.1371/journal.pone.0303783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 04/30/2024] [Indexed: 05/26/2024] Open
Abstract
Potato is considered a key component of the global food system and plays a vital role in strengthening world food security. A major constraint to potato production worldwide is the Potato Virus Y (PVY), belonging to the genus Potyvirus in the family of Potyviridae. Selective breeding of potato with resistance to PVY pathogens remains the best method to limit the impact of viral infections. Understanding the genetic diversity and population structure of potato germplasm is important for breeders to improve new cultivars for the sustainable use of genetic materials in potato breeding to PVY pathogens. While, genetic diversity improvement in modern potato breeding is facing increasingly narrow genetic basis and the decline of the genetic diversity. In this research, we performed genotyping-by-sequencing (GBS)-based diversity analysis on 10 commercial potato cultivars and weighted gene co-expression network analysis (WGCNA) to identify candidate genes related to PVY-resistance. WGCNA is a system biology technique that uses the WGCNA R software package to describe the correlation patterns between genes in multiple samples. In terms of consumption, these cultivars are a high rate among Iranian people. Using population structure analysis, the 10 cultivars were clustered into three groups based on the 118343 single nucleotide polymorphisms (SNPs) generated by GBS. Read depth ranged between 5 and 18. The average data size and Q30 of the reads were 145.98 Mb and 93.63%, respectively. Based on the WGCNA and gene expression analysis, the StDUF538, StGTF3C5, and StTMEM161A genes were associated with PVY resistance in the potato genome. Further, these three hub genes were significantly involved in defense mechanism where the StTMEM161A was involved in the regulation of alkalization apoplast, the StDUF538 was activated in the chloroplast degradation program, and the StGTF3C5 regulated the proteins increase related to defense in the PVY infected cells. In addition, in the genetic improvement programs, these hub genes can be used as genetic markers for screening commercial cultivars for PVY resistance. Our survey demonstrated that the combination of GBS-based genetic diversity germplasm analysis and WGCNA can assist breeders to select cultivars resistant to PVY as well as help design proper crossing schemes in potato breeding.
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Affiliation(s)
- Zahra Hajibarat
- Faculty of Life Sciences & Biotechnology, Department of Cell & Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | - Abbas Saidi
- Faculty of Life Sciences & Biotechnology, Department of Cell & Molecular Biology, Shahid Beheshti University, Tehran, Iran
| | - Mehrshad Zeinalabedini
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Ahmad Mousapour Gorji
- Department of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Mohammad Reza Ghaffari
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Vahid Shariati
- National Institute of Genetic Engineering and Biotechnology, NIGEB Genome Center, Tehran, Iran
| | - Rahim Ahmadvand
- Department of Vegetable Research, Seed and Plant Improvement Institute (SPII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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Song J, Liu Y, Guo R, Pacheco A, Muñoz-Zavala C, Song W, Wang H, Cao S, Hu G, Zheng H, Dhliwayo T, San Vicente F, Prasanna BM, Wang C, Zhang X. Exploiting genomic tools for genetic dissection and improving the resistance to Fusarium stalk rot in tropical maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:109. [PMID: 38649662 DOI: 10.1007/s00122-024-04597-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/07/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE A stable genomic region conferring FSR resistance at ~250 Mb on chromosome 1 was identified by GWAS. Genomic prediction has the potential to improve FSR resistance. Fusarium stalk rot (FSR) is a global destructive disease in maize; the efficiency of phenotypic selection for improving FSR resistance was low. Novel genomic tools of genome-wide association study (GWAS) and genomic prediction (GP) provide an opportunity for genetic dissection and improving FSR resistance. In this study, GWAS and GP analyses were performed on 562 tropical maize inbred lines consisting of two populations. In total, 15 SNPs significantly associated with FSR resistance were identified across two populations and the combinedPOP consisting of all 562 inbred lines, with the P-values ranging from 1.99 × 10-7 to 8.27 × 10-13, and the phenotypic variance explained (PVE) values ranging from 0.94 to 8.30%. The genetic effects of the 15 favorable alleles ranged from -4.29 to -14.21% of the FSR severity. One stable genomic region at ~ 250 Mb on chromosome 1 was detected across all populations, and the PVE values of the SNPs detected in this region ranged from 2.16 to 5.18%. Prediction accuracies of FSR severity estimated with the genome-wide SNPs were moderate and ranged from 0.29 to 0.51. By incorporating genotype-by-environment interaction, prediction accuracies were improved between 0.36 and 0.55 in different breeding scenarios. Considering both the genome coverage and the threshold of the P-value of SNPs to select a subset of molecular markers further improved the prediction accuracies. These findings extend the knowledge of exploiting genomic tools for genetic dissection and improving FSR resistance in tropical maize.
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Affiliation(s)
- Junqiao Song
- Henan University of Science and Technology, Luoyang, 471000, Henan, China
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yubo Liu
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 200063, China
| | - Rui Guo
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Angela Pacheco
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Carlos Muñoz-Zavala
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Wei Song
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Hui Wang
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 200063, China
| | - Shiliang Cao
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, 150070, Heilongjiang, China
| | - Guanghui Hu
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, 150070, Heilongjiang, China
| | - Hongjian Zheng
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 200063, China
| | - Thanda Dhliwayo
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Felix San Vicente
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, Nairobi, 00621, Kenya
| | - Chunping Wang
- Henan University of Science and Technology, Luoyang, 471000, Henan, China.
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico.
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China.
- Nanfan Research Institute, CAAS, Sanya, 572024, Hainan, China.
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3
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Fofana B, Soto-Cerda B, Zaidi M, Main D, Fillmore S. Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes. Front Genet 2024; 14:1306519. [PMID: 38357658 PMCID: PMC10864671 DOI: 10.3389/fgene.2023.1306519] [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: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 02/16/2024] Open
Abstract
Cultivated potato (Solanum tuberosum) is known to be highly susceptible to drought. With climate change and its frequent episodes of drought, potato growers will face increased challenges to achieving their yield goals. Currently, a high proportion of untapped potato germplasm remains within the diploid potato relatives, and the genetic architecture of the drought tolerance and maturity traits of diploid potatoes is still unknown. As such, a panel of 384 ethyl methanesulfonate-mutagenized diploid potato clones were evaluated for drought tolerance and plant maturity under field conditions. Genome-wide association studies (GWAS) were conducted to dissect the genetic architecture of the traits. The results obtained from the genetic structure analysis of the panel showed five main groups and seven subgroups. Using the Genome Association and Prediction Integrated Tool-mixed linear model GWAS statistical model, 34 and 17 significant quantitative trait nucleotides (QTNs) were found associated with maturity and drought traits, respectively. Chromosome 5 carried most of the QTNs, some of which were also detected by using the restricted two-stage multi-locus multi-allele-GWAS haploblock-based model, and two QTNs were found to be pleiotropic for both maturity and drought traits. Using the non-parametric U-test, one and three QTNs, with 5.13%-7.4% phenotypic variations explained, showed favorable allelic effects that increase the maturity and drought trait values. The quantitaive trait loci (QTLs)/QTNs associated with maturity and drought trait were found co-located in narrow (0.5-1 kb) genomic regions with 56 candidate genes playing roles in plant development and senescence and in abiotic stress responses. A total of 127 potato clones were found to be late maturing and tolerant to drought, while nine were early to moderate-late maturing and tolerant to drought. Taken together, the data show that the studied germplasm panel and the identified candidate genes are prime genetic resources for breeders and biologists in conventional breeding and targeted gene editing as climate adaptation tools.
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Affiliation(s)
- Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Braulio Soto-Cerda
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Temuco, Chile
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Moshin Zaidi
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - David Main
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Sherry Fillmore
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
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Hadebe MT, Malgwi SA, Okpeku M. Revolutionizing Malaria Vector Control: The Importance of Accurate Species Identification through Enhanced Molecular Capacity. Microorganisms 2023; 12:82. [PMID: 38257909 PMCID: PMC10818655 DOI: 10.3390/microorganisms12010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/08/2023] [Accepted: 12/20/2023] [Indexed: 01/24/2024] Open
Abstract
Many factors, such as the resistance to pesticides and a lack of knowledge of the morphology and molecular structure of malaria vectors, have made it more challenging to eradicate malaria in numerous malaria-endemic areas of the globe. The primary goal of this review is to discuss malaria vector control methods and the significance of identifying species in vector control initiatives. This was accomplished by reviewing methods of molecular identification of malaria vectors and genetic marker classification in relation to their use for species identification. Due to its specificity and consistency, molecular identification is preferred over morphological identification of malaria vectors. Enhanced molecular capacity for species identification will improve mosquito characterization, leading to accurate control strategies/treatment targeting specific mosquito species, and thus will contribute to malaria eradication. It is crucial for disease epidemiology and surveillance to accurately identify the Plasmodium spp. that are causing malaria in patients. The capacity for disease surveillance will be significantly increased by the development of more accurate, precise, automated, and high-throughput diagnostic techniques. In conclusion, although morphological identification is quick and achievable at a reduced cost, molecular identification is preferred for specificity and sensitivity. To achieve the targeted malaria elimination goal, proper identification of vectors using accurate techniques for effective control measures should be prioritized.
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Affiliation(s)
| | | | - Moses Okpeku
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
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Pronozin AY, Salina EA, Afonnikov DA. GBS-DP: a bioinformatics pipeline for processing data coming from genotyping by sequencing. Vavilovskii Zhurnal Genet Selektsii 2023; 27:737-745. [PMID: 38213704 PMCID: PMC10777284 DOI: 10.18699/vjgb-23-86] [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: 07/21/2023] [Revised: 09/08/2023] [Accepted: 09/09/2023] [Indexed: 01/13/2024] Open
Abstract
The development of next-generation sequencing technologies has provided new opportunities for genotyping various organisms, including plants. Genotyping by sequencing (GBS) is used to identify genetic variability more rapidly, and is more cost-effective than whole-genome sequencing. GBS has demonstrated its reliability and flexibility for a number of plant species and populations. It has been applied to genetic mapping, molecular marker discovery, genomic selection, genetic diversity studies, variety identification, conservation biology and evolutionary studies. However, reduction in sequencing time and cost has led to the need to develop efficient bioinformatics analyses for an ever-expanding amount of sequenced data. Bioinformatics pipelines for GBS data analysis serve the purpose. Due to the similarity of data processing steps, existing pipelines are mainly characterised by a combination of software packages specifically selected either to process data for certain organisms or to process data from any organisms. However, despite the usage of efficient software packages, these pipelines have some disadvantages. For example, there is a lack of process automation (in some pipelines, each step must be started manually), which significantly reduces the performance of the analysis. In the majority of pipelines, there is no possibility of automatic installation of all necessary software packages; for most of them, it is also impossible to switch off unnecessary or completed steps. In the present work, we have developed a GBS-DP bioinformatics pipeline for GBS data analysis. The pipeline can be applied for various species. The pipeline is implemented using the Snakemake workflow engine. This implementation allows fully automating the process of calculation and installation of the necessary software packages. Our pipeline is able to perform analysis of large datasets (more than 400 samples).
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Affiliation(s)
- A Y Pronozin
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia
| | - E A Salina
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State Agrarian University, Novosibirsk, Russia
| | - D A Afonnikov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Kurchatov Genomic Center of ICG SB RAS, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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6
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Omondi DO, Dida MM, Berger DK, Beyene Y, Nsibo DL, Juma C, Mahabaleswara SL, Gowda M. Combination of linkage and association mapping with genomic prediction to infer QTL regions associated with gray leaf spot and northern corn leaf blight resistance in tropical maize. Front Genet 2023; 14:1282673. [PMID: 38028598 PMCID: PMC10661943 DOI: 10.3389/fgene.2023.1282673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
Among the diseases threatening maize production in Africa are gray leaf spot (GLS) caused by Cercospora zeina and northern corn leaf blight (NCLB) caused by Exserohilum turcicum. The two pathogens, which have high genetic diversity, reduce the photosynthesizing ability of susceptible genotypes and, hence, reduce the grain yield. To identify population-based quantitative trait loci (QTLs) for GLS and NCLB resistance, a biparental population of 230 lines derived from the tropical maize parents CML511 and CML546 and an association mapping panel of 239 tropical and sub-tropical inbred lines were phenotyped across multi-environments in western Kenya. Based on 1,264 high-quality polymorphic single-nucleotide polymorphisms (SNPs) in the biparental population, we identified 10 and 18 QTLs, which explained 64.2% and 64.9% of the total phenotypic variance for GLS and NCLB resistance, respectively. A major QTL for GLS, qGLS1_186 accounted for 15.2% of the phenotypic variance, while qNCLB3_50 explained the most phenotypic variance at 8.8% for NCLB resistance. Association mapping with 230,743 markers revealed 11 and 16 SNPs significantly associated with GLS and NCLB resistance, respectively. Several of the SNPs detected in the association panel were co-localized with QTLs identified in the biparental population, suggesting some consistent genomic regions across genetic backgrounds. These would be more relevant to use in field breeding to improve resistance to both diseases. Genomic prediction models trained on the biparental population data yielded average prediction accuracies of 0.66-0.75 for the disease traits when validated in the same population. Applying these prediction models to the association panel produced accuracies of 0.49 and 0.75 for GLS and NCLB, respectively. This research conducted in maize fields relevant to farmers in western Kenya has combined linkage and association mapping to identify new QTLs and confirm previous QTLs for GLS and NCLB resistance. Overall, our findings imply that genetic gain can be improved in maize breeding for resistance to multiple diseases including GLS and NCLB by using genomic selection.
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Affiliation(s)
- Dennis O. Omondi
- Department of Crops and Soil Sciences, School of Agriculture, Food Security and Environmental Sciences, Maseno University, Kisumu, Kenya
- Crop Science Division Bayer East Africa Limited, Nairobi, Kenya
| | - Mathews M. Dida
- Department of Crops and Soil Sciences, School of Agriculture, Food Security and Environmental Sciences, Maseno University, Kisumu, Kenya
| | - Dave K. Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Yoseph Beyene
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - David L. Nsibo
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Collins Juma
- Crop Science Division Bayer East Africa Limited, Nairobi, Kenya
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Suresh L. Mahabaleswara
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | - Manje Gowda
- The Global Maize Program, International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
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7
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Anirban A, Masouleh AK, Henry RJ, O'Hare TJ. Sequence variations associated with novel purple-pericarp super-sweetcorn compared to its purple-pericarp maize and white super-sweetcorn parents. Mol Genet Genomics 2023; 298:1395-1405. [PMID: 37679604 PMCID: PMC10657292 DOI: 10.1007/s00438-023-02060-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/06/2023] [Indexed: 09/09/2023]
Abstract
Recently, a novel purple-pericarp super-sweetcorn line, 'Tim1' (A1A1.sh2sh2) was derived from the purple-pericarp maize 'Costa Rica' (A1Sh2.A1Sh2) and white shrunken2 (sh2) super-sweetcorn 'Tims-white' (a1sh2.a1sh2), however, information regarding anthocyanin biosynthesis genes controlling purple colour and sweetness gene is lacking. Specific sequence differences in the CDS (coding DNA sequence) and promoter regions of the anthocyanin biosynthesis structural genes, anthocyanin1 (A1), purple aleurone1 (Pr1) and regulatory genes, purple plant1 (Pl1), plant colour1 (B1), coloured1 (R1), and the sweetcorn structural gene, shrunken2 (sh2) were investigated using the publicly available annotated yellow starchy maize, B73 (NAM5.0) as a reference genome. In the CDS region, the A1, Pl1 and R1 gene sequence differences of 'Tim1' and 'Costa Rica' were similar, as they control purple-pericarp pigmentation. However, the B1 gene showed similarity between the 'Tim1' and 'Tims-white' lines, which may indicate that it does not have a role in controlling pericarp colour, unlike the report of a previous study. In the case of the Pr1 gene, in contrast to 'Costa Rica', 6- and 8-bp dinucleotide (TA) repeats were observed in the promoter region of the 'Tims-white' and 'Tim1' lines, respectively, indicating the defective functionality (redder colour in 'Tim1' rather than purple in 'Costa Rica') of the recessive pr1 allele. In sweetcorn, the structural gene (sh2), sequence showed similarity between purple-sweet 'Tim1' and its white-sweet parent 'Tims-white', as both display a shrunken phenotype in their mature kernels. These findings revealed that the developed purple-sweet line is different to the reference yellow-nonsweet line in both the anthocyanin biosynthesis and sweetcorn genes.
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Affiliation(s)
- Apurba Anirban
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Australia.
| | | | - Robert J Henry
- Centre for Crop Science, QAAFI, The University of Queensland, Brisbane, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, The University of Queensland, Brisbane, Australia
| | - Tim J O'Hare
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Brisbane, Australia
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Hossain F, Jaiswal SK, Muthusamy V, Zunjare RU, Mishra SJ, Chand G, Bhatt V, Bhat JS, Das AK, Chauhan HS, Gupta HS. Enhancement of nutritional quality in maize kernel through marker-assisted breeding for vte4, crtRB1, and opaque2 genes. J Appl Genet 2023; 64:431-443. [PMID: 37450243 DOI: 10.1007/s13353-023-00768-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 05/31/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Traditional maize is poor in vitamin-E [α-tocopherol (α-T): 6-8 ppm], vitamin-A [provitamin-A (proA): 1-2ppm], lysine (0.150-0.2-50%), and tryptophan (0.030-0.040%). Here, we combined favourable alleles of vte4, crtRB1, and opaque2 (o2) genes in the parents of maize hybrids, viz., APQH-10 (PMI-PV-9 × PMI-PV-14) and APQH-11 (PMI-PV-9 × PMI-PV-15) using molecular breeding. Gene-specific markers were successfully used to select vte4, crtRB1, and o2 in BC1F1, BC2F1, and BC2F2 generations. Simple sequence repeats (104-109) were used for background selection, leading to an average recovery of 94% recurrent parent genome. The introgressed inbreds possessed significantly higher α-T: 18.38 ppm, α-/γ-tocopherol (α-/γ-T: 52%), and α-/total tocopherol (α-/TT: 32%) compared to original inbreds (α-T: 8.17 ppm, α-/γ-T: 25%, α-/TT: 18%). These newly derived inbreds also possessed higher β-carotene (BC: 8.91 ppm), β-cryptoxanthin (BCX: 1.27 ppm), proA (9.54 ppm), lysine (0.348%), and tryptophan (0.082%) compared to traditional maize inbreds. The reconstituted hybrids recorded higher α-T (2.1-fold), α-/γ-T (1.9-fold), and α-/TT (1.6-fold) over the original hybrids. These reconstituted hybrids were also rich in BC (5.7-fold), BCX (3.3-fold), proA (5.3-fold), lysine (1.9-fold), and tryptophan (2.0-fold) over the traditional hybrids. The reconstituted hybrids had similar grain yield and phenotypic characteristics to original versions. These multinutrient-rich maize hybrids hold great potential to alleviate malnutrition in sustainable and cost-effective manner.
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Affiliation(s)
- Firoz Hossain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Sunil K Jaiswal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vignesh Muthusamy
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rajkumar U Zunjare
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Subhra J Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gulab Chand
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Vinay Bhatt
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Jayant S Bhat
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Abhijit K Das
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Hema S Chauhan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Hari S Gupta
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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9
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Moravčíková N, Kasarda R, Židek R, McEwan JC, Brauning R, Landete-Castillejos T, Chonco L, Ciberej J, Pokorádi J. Traces of Human-Mediated Selection in the Gene Pool of Red Deer Populations. Animals (Basel) 2023; 13:2525. [PMID: 37570333 PMCID: PMC10417186 DOI: 10.3390/ani13152525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 07/27/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
In this study, we analysed the effect of human-mediated selection on the gene pool of wild and farmed red deer populations based on genotyping-by-sequencing data. The farmed red deer sample covered populations spread across seven countries and two continents (France, Germany, Hungary, Latvia, New Zealand, Poland, and Slovakia). The Slovak and Spain wild red deer populations (the latter one in a large game estate) were used as control outgroups. The gene flow intensity, relationship and admixture among populations were tested by the Bayesian approach and discriminant analysis of principal components (DAPC). The highest gene diversity (He = 0.19) and the lowest genomic inbreeding (FHOM = 0.04) found in Slovak wild population confirmed our hypothesis that artificial selection accompanied by bottlenecks has led to the increase in overall genomic homozygosity. The Bayesian approach and DAPC consistently identified three separate genetic groups. As expected, the farmed populations were clustered together, while the Slovak and Spanish populations formed two separate clusters. Identified traces of genetic admixture in the gene pool of farmed populations reflected a strong contemporary migration rate between them. This study suggests that even if the history of deer farming has been shorter than traditional livestock species, it may leave significant traces in the genome structure.
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Affiliation(s)
- Nina Moravčíková
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - Radovan Kasarda
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - Radoslav Židek
- Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, 949 76 Nitra, Slovakia;
| | - John Colin McEwan
- AgResearch, Invermay Agricultural Research Centre, Mosgiel 9024, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Research Centre, Mosgiel 9024, New Zealand; (J.C.M.); (R.B.)
| | - Tomás Landete-Castillejos
- Instituto de Recursos Cinegéticos-Instituto de Desarrollo Regional, University of Castilla-La Mancha, 02071 Albacete, Spain; (T.L.-C.); (L.C.)
| | - Louis Chonco
- Instituto de Recursos Cinegéticos-Instituto de Desarrollo Regional, University of Castilla-La Mancha, 02071 Albacete, Spain; (T.L.-C.); (L.C.)
| | - Juraj Ciberej
- Department of Breeding and Diseases of Game, Fish and Bees, Ecology and Cynology, University of Veterinary Medicine and Pharmacy, 041 81 Košice, Slovakia
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Machado IP, DoVale JC, Sabadin F, Fritsche-Neto R. On the usefulness of mock genomes to define heterotic pools, testers, and hybrid predictions in orphan crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1164555. [PMID: 37332727 PMCID: PMC10272588 DOI: 10.3389/fpls.2023.1164555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/10/2023] [Indexed: 06/20/2023]
Abstract
The advances in genomics in recent years have increased the accuracy and efficiency of breeding programs for many crops. Nevertheless, the adoption of genomic enhancement for several other crops essential in developing countries is still limited, especially for those that do not have a reference genome. These crops are more often called orphans. This is the first report to show how the results provided by different platforms, including the use of a simulated genome, called the mock genome, can generate in population structure and genetic diversity studies, especially when the intention is to use this information to support the formation of heterotic groups, choice of testers, and genomic prediction of single crosses. For that, we used a method to assemble a reference genome to perform the single-nucleotide polymorphism (SNP) calling without needing an external genome. Thus, we compared the analysis results using the mock genome with the standard approaches (array and genotyping-by-sequencing (GBS)). The results showed that the GBS-Mock presented similar results to the standard methods of genetic diversity studies, division of heterotic groups, the definition of testers, and genomic prediction. These results showed that a mock genome constructed from the population's intrinsic polymorphisms to perform the SNP calling is an effective alternative for conducting genomic studies of this nature in orphan crops, especially those that do not have a reference genome.
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Affiliation(s)
| | - Júlio César DoVale
- Department of Crop Science, Federal University of Ceará, Fortaleza, Brazil
| | - Felipe Sabadin
- School of Plant and Environmental Sciences, Virginia Tech: Virginia Polytechnic Institute and State University, Blacksburg, VA, United States
| | - Roberto Fritsche-Neto
- LSU AgCenter, Louisiana State University Agricultural Center, Baton Rouge, LA, United States
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Chen S, Dang D, Liu Y, Ji S, Zheng H, Zhao C, Dong X, Li C, Guan Y, Zhang A, Ruan Y. Genome-wide association study presents insights into the genetic architecture of drought tolerance in maize seedlings under field water-deficit conditions. FRONTIERS IN PLANT SCIENCE 2023; 14:1165582. [PMID: 37223800 PMCID: PMC10200999 DOI: 10.3389/fpls.2023.1165582] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/24/2023] [Indexed: 05/25/2023]
Abstract
Introduction Drought stress is one of the most serious abiotic stresses leading to crop yield reduction. Due to the wide range of planting areas, the production of maize is particularly affected by global drought stress. The cultivation of drought-resistant maize varieties can achieve relatively high, stable yield in arid and semi-arid zones and in the erratic rainfall or occasional drought areas. Therefore, to a great degree, the adverse impact of drought on maize yield can be mitigated by developing drought-resistant or -tolerant varieties. However, the efficacy of traditional breeding solely relying on phenotypic selection is not adequate for the need of maize drought-resistant varieties. Revealing the genetic basis enables to guide the genetic improvement of maize drought tolerance. Methods We utilized a maize association panel of 379 inbred lines with tropical, subtropical and temperate backgrounds to analyze the genetic structure of maize drought tolerance at seedling stage. We obtained the high quality 7837 SNPs from DArT's and 91,003 SNPs from GBS, and a resultant combination of 97,862 SNPs of GBS with DArT's. The maize population presented the lower her-itabilities of the seedling emergence rate (ER), seedling plant height (SPH) and grain yield (GY) under field drought conditions. Results GWAS analysis by MLM and BLINK models with the phenotypic data and 97862 SNPs revealed 15 variants that were significantly independent related to drought-resistant traits at the seedling stage above the threshold of P < 1.02 × 10-5. We found 15 candidate genes for drought resistance at the seedling stage that may involve in (1) metabolism (Zm00001d012176, Zm00001d012101, Zm00001d009488); (2) programmed cell death (Zm00001d053952); (3) transcriptional regulation (Zm00001d037771, Zm00001d053859, Zm00001d031861, Zm00001d038930, Zm00001d049400, Zm00001d045128 and Zm00001d043036); (4) autophagy (Zm00001d028417); and (5) cell growth and development (Zm00001d017495). The most of them in B73 maize line were shown to change the expression pattern in response to drought stress. These results provide useful information for understanding the genetic basis of drought stress tolerance of maize at seedling stage.
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Affiliation(s)
- Shan Chen
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Dongdong Dang
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shang-hai Academy of Agricultural Sciences, Shanghai, China
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Yubo Liu
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shang-hai Academy of Agricultural Sciences, Shanghai, China
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Shuwen Ji
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Hongjian Zheng
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shang-hai Academy of Agricultural Sciences, Shanghai, China
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Chenghao Zhao
- Dandong Academy of Agricultural Sciences, Fengcheng, Liaoning, China
| | - Xiaomei Dong
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Cong Li
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yuan Guan
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shang-hai Academy of Agricultural Sciences, Shanghai, China
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Ao Zhang
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
| | - Yanye Ruan
- Shenyang City Key Laboratory of Maize Genomic Selection Breeding, College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning, China
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Tympakianakis S, Trantas E, Avramidou EV, Ververidis F. Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1139647. [PMID: 37180393 PMCID: PMC10169827 DOI: 10.3389/fpls.2023.1139647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023]
Abstract
The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.
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Affiliation(s)
- Stylianos Tympakianakis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
| | - Emmanouil Trantas
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
| | - Evangelia V. Avramidou
- Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organisation “DIMITRA“, Athens, Greece
| | - Filippos Ververidis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
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Kang H, An SM, Park YJ, Lee YB, Lee JH, Cheon KS, Kim KA. Population Genomics Study and Implications for the Conservation of Zabelia tyaihyonii Based on Genotyping-By-Sequencing. PLANTS (BASEL, SWITZERLAND) 2022; 12:171. [PMID: 36616299 PMCID: PMC9823854 DOI: 10.3390/plants12010171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/26/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
Zabelia tyaihyonii (Nakai) Hisauti and H. Hara is a perennial shrub endemic to Republic of Korea that grows naturally in only a very limited region of the dolomite areas of Gangwon-do and Chungcheongbuk-do Provinces in the Republic of Korea. Given its geographical characteristics, it is more vulnerable than more widely distributed species. Despite the need for comprehensive information to support conservation, population genetic information for this species is very scarce. In this study, we analyzed the genetic diversity and population structure of 94 individuals from six populations of Z. tyaihyonii using a genotyping-by-sequencing (GBS) approach to provide important information for proper conservation and management. Our results, based on 3088 single nucleotide polymorphisms (SNPs), showed a mean expected heterozygosity (He) of 0.233, no sign of within-population inbreeding (GIS that was close to or even below zero in all populations), and a high level of genetic differentiation (FST = 0.170). Analysis of molecular variance (AMOVA) indicated that the principal molecular variance existed within populations (84.5%) rather than among populations (17.0%). We suggested that six management units were proposed for conservation considering Bayesian structure analysis and phylogenetic analysis, and given the various current situations faced by Z. tyaihyonii, it is believed that not only the in situ conservation but also the ex situ conservation should be considered.
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Affiliation(s)
- Halam Kang
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Sung-Mo An
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Yoo-Jung Park
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Yoo-Bin Lee
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Jung-Hyun Lee
- Department of Biology Education, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kyeong-Sik Cheon
- Department of Biological Science, Sangji University, Wonju 26339, Republic of Korea
| | - Kyung-Ah Kim
- Environmental Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
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Qu J, Chassaigne-Ricciulli AA, Fu F, Yu H, Dreher K, Nair SK, Gowda M, Beyene Y, Makumbi D, Dhliwayo T, Vicente FS, Olsen M, Prasanna BM, Li W, Zhang X. Low-Density Reference Fingerprinting SNP Dataset of CIMMYT Maize Lines for Quality Control and Genetic Diversity Analyses. PLANTS (BASEL, SWITZERLAND) 2022; 11:3092. [PMID: 36432819 PMCID: PMC9697014 DOI: 10.3390/plants11223092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
CIMMYT maize lines (CMLs), which represent the tropical maize germplasm, are freely available worldwide. All currently released 615 CMLs and fourteen temperate maize inbred lines were genotyped with 180 kompetitive allele-specific PCR single nucleotide polymorphisms to develop a reference fingerprinting SNP dataset that can be used to perform quality control (QC) and genetic diversity analyses. The QC analysis identified 25 CMLs with purity, identity, or mislabeling issues. Further field observation, purification, and re-genotyping of these CMLs are required. The reference fingerprinting SNP dataset was developed for all of the currently released CMLs with 152 high-quality SNPs. The results of principal component analysis and average genetic distances between subgroups showed a clear genetic divergence between temperate and tropical maize, whereas the three tropical subgroups partially overlapped with one another. More than 99% of the pairs of CMLs had genetic distances greater than 0.30, showing their high genetic diversity, and most CMLs are distantly related. The heterotic patterns, estimated with the molecular markers, are consistent with those estimated using pedigree information in two major maize breeding programs at CIMMYT. These research findings are helpful for ensuring the regeneration and distribution of the true CMLs, via QC analysis, and for facilitating the effective utilization of the CMLs, globally.
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Affiliation(s)
- Jingtao Qu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, Mexico
| | | | - Fengling Fu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Haoqiang Yu
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Kate Dreher
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, Mexico
| | - Sudha K. Nair
- Asia Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Hyderabad 502324, Telangana, India
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, Kenya
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, Kenya
| | - Dan Makumbi
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, Kenya
| | - Thanda Dhliwayo
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, Mexico
| | - Felix San Vicente
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, Mexico
| | - Michael Olsen
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, Kenya
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P.O. Box 1041, Nairobi 00621, Kenya
| | - Wanchen Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco 56237, Mexico
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15
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Sahu TK, Singh AK, Mittal S, Jha SK, Kumar S, Jacob SR, Singh K. G-DIRT: a web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data. Brief Bioinform 2022; 23:6678959. [PMID: 36040109 DOI: 10.1093/bib/bbac348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/11/2022] [Accepted: 07/26/2022] [Indexed: 01/26/2023] Open
Abstract
Maintaining duplicate germplasms in genebanks hampers effective conservation and utilization of genebank resources. The redundant germplasm adds to the cost of germplasm conservation by requiring a large proportion of the genebank financial resources towards conservation rather than enriching the diversity. Besides, genome-wide-association analysis using an association panel with over-represented germplasms can be biased resulting in spurious marker-trait associations. The conventional methods of germplasm duplicate removal using passport information suffer from incomplete or missing passport information and data handling errors at various stages of germplasm enrichment. This limitation is less likely in the case of genotypic data. Therefore, we developed a web-based tool, Germplasm Duplicate Identification and Removal Tool (G-DIRT), which allows germplasm duplicate identification based on identity-by-state analysis using single-nucleotide polymorphism genotyping information along with pre-processing of genotypic data. A homozygous genotypic difference threshold of 0.1% for germplasm duplicates has been determined using tetraploid wheat genotypic data with 94.97% of accuracy. Based on the genotypic difference, the tool also builds a dendrogram that can visually depict the relationship between genotypes. To overcome the constraint of high-dimensional genotypic data, an offline version of G-DIRT in the interface of R has also been developed. The G-DIRT is expected to help genebank curators, breeders and other researchers across the world in identifying germplasm duplicates from the global genebank collections by only using the easily sharable genotypic data instead of physically exchanging the seeds or propagating materials. The web server will complement the existing methods of germplasm duplicate identification based on passport or phenotypic information being freely accessible at http://webtools.nbpgr.ernet.in/gdirt/.
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Affiliation(s)
- Tanmaya Kumar Sahu
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | - Shikha Mittal
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | | | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | - Sherry Rachel Jacob
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India.,ICAR- Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India.,International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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16
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He J, He Z, Yang D, Ma Z, Chen H, Zhang Q, Deng F, Ye L, Pu Y, Zhang M, Yang S, Yang S, Yan T. Genetic Variation in Schizothorax kozlovi Nikolsky in the Upper Reaches of the Chinese Yangtze River Based on Genotyping for Simplified Genome Sequencing. Animals (Basel) 2022; 12:ani12172181. [PMID: 36077902 PMCID: PMC9454844 DOI: 10.3390/ani12172181] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/23/2022] Open
Abstract
Simple Summary Schizothorax kozlovi Nikolsky is a unique cold−water fish in the upper reaches of the Yangtze River in China and has high economic value. In our study, genetic diversity and population structure analyses were performed on seven wild populations in the upper reaches of the Yangtze River by GBS. The above results indicate that the populations of S. kozlovi have different degrees of tolerance and selection pressure in response to temperature and altitude. The Wujiang population was genetically differentiated from the Jinsha River and Yalong River populations. The Wujiang intrapopulation has greater genetic diversity and differentiation than the Jinsha River and Yalong River populations, which demonstrates that the Jinsha and Yalong populations require more attention and resources for their protection. The results of this study will increase our understanding of the diversity of S. kozlovi in the upper reaches of the Yangtze River and provide a basis for the conservation and utilization of wild resources. Abstract Schizothorax kozlovi Nikolsky is a unique cold−water fish in the upper reaches of the Yangtze River in China and has high economic value. In our study, genetic diversity and population structure analyses were performed on seven wild populations (originating from the Jinsha River, Yalong River, and Wujiang River) in the upper reaches of the Yangtze River by genotyping by sequencing (GBS). The results indicated that a total of 303,970 single−nucleotide polymorphisms (SNPs) were identified from the seven wild populations. Lower genetic diversity was exhibited among the intrapopulations of the three tributaries, and the Wujiang River population had significant genetic differentiation when compared to the Jinsha River and Yalong River populations. Furthermore, the selected SNPs were enriched in cellular processes, environmental adaptation, signal transduction, and related metabolic processes between the Wujiang population and the other two populations. The above results indicate that the populations of S. kozlovi have different degrees of tolerance and selection pressure in response to temperature and altitude. The Wujiang intrapopulation has greater genetic diversity and differentiation than the Jinsha River and Yalong River populations, which demonstrates that the Jinsha and Yalong populations require more attention and resources for their protection. The results of this study will increase our understanding of the diversity of S. kozlovi in the upper reaches of the Yangtze River and provide a basis for the conservation and utilization of wild resources.
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Martínez-Fortún J, Phillips DW, Jones HD. Natural and artificial sources of genetic variation used in crop breeding: A baseline comparator for genome editing. Front Genome Ed 2022; 4:937853. [PMID: 36072906 PMCID: PMC9441798 DOI: 10.3389/fgeed.2022.937853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/13/2022] [Indexed: 11/13/2022] Open
Abstract
Traditional breeding has successfully selected beneficial traits for food, feed, and fibre crops over the last several thousand years. The last century has seen significant technological advancements particularly in marker assisted selection and the generation of induced genetic variation, including over the last few decades, through mutation breeding, genetic modification, and genome editing. While regulatory frameworks for traditional varietal development and for genetic modification with transgenes are broadly established, those for genome editing are lacking or are still evolving in many regions. In particular, the lack of “foreign” recombinant DNA in genome edited plants and that the resulting SNPs or INDELs are indistinguishable from those seen in traditional breeding has challenged development of new legislation. Where products of genome editing and other novel breeding technologies possess no transgenes and could have been generated via traditional methods, we argue that it is logical and proportionate to apply equivalent legislative oversight that already exists for traditional breeding and novel foods. This review analyses the types and the scale of spontaneous and induced genetic variation that can be selected during traditional plant breeding activities. It provides a base line from which to judge whether genetic changes brought about by techniques of genome editing or other reverse genetic methods are indeed comparable to those routinely found using traditional methods of plant breeding.
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Decoupling in Diversification and Body Size Rates During the Radiation of Phyllodactylus: Evidence Suggests Minor Role of Ecology in Shaping Phenotypes. Evol Biol 2022. [DOI: 10.1007/s11692-022-09575-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Nyirahabimana F, Shimira F, Zahid G, Solmaz I. Recent status of Genotyping by Sequencing (GBS) Technology in cucumber (Cucumis sativus L.): a review. Mol Biol Rep 2022; 49:5547-5554. [PMID: 35596053 DOI: 10.1007/s11033-022-07469-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/21/2022] [Accepted: 04/08/2022] [Indexed: 01/27/2023]
Abstract
Current and advanced breeding tools are being used to improve economically important horticultural crops to meet the consumers' needs and preferences. Genotyping-by-sequencing (GBS) is an extremely useful tool in the investigation and analysis of the genetic diversity of different cultivars. Based on a broad range of genetic backgrounds like single nucleotide polymorphism (SNPs), GBS is known as a novel technique to facilitate the detection of quantitative trait loci (QTL) regions robustly linked with interested traits compared to genome-wide association study (GWAS) and QTL. GBS has gained popularity among breeders in recent years and it is also employed in cucumber breeding programs. Cucumbers (C. sativus L.) are monoecious, gynoecious and some of them are parthenocarpic species. Cucumber is one of the most economical and essential crops in the Cucurbitaceae family. For time immemorial, cucumber has been produced and consumed all over the world like other cucurbits. To a large extent, cultivated cucurbits are beneficial to human health for providing necessary minerals and fibers.Therefore, this review portrays the current status of advances made by using GBS and its combination with other tools in various studies of cucumber such as the use of GBS and single nucleotide polymorphism (SNP) markers, GBS and GWAS, also with QTL and marker-assisted selection (MAS) are applied to display and detect explicit genetic architecture complex traits in crops and chromosome rearrangements.Cucumber breeding programs have undoubtedly benefited from genotyping-by-sequencing. Using the GBS method, research discovered lots of new candidate genes that control various traits including spine color, fruit stalk-end color, and disease resistance in cucumber lines.
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Affiliation(s)
- Fildaus Nyirahabimana
- Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Turkey.
| | - Flavien Shimira
- Department of Horticulture, Faculty of Agriculture, Çukurova University, 01330, Adana, Turkey
| | - Ghassan Zahid
- Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Turkey
| | - Ilknur Solmaz
- Department of Biotechnology, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Turkey
- Department of Horticulture, Faculty of Agriculture, Çukurova University, 01330, Adana, Turkey
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Klees S, Heinrich F, Schmitt AO, Gültas M. agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species. BIOLOGY 2022; 11:biology11050684. [PMID: 35625412 PMCID: PMC9138521 DOI: 10.3390/biology11050684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/25/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022]
Abstract
Simple Summary In breeding research, the investigation of regulatory SNPs (rSNPs) is becoming increasingly important due to their potential causal role for specific functional traits. Especially for crop species, there is still a lack of systematic analyses to detect rSNPs and their predicted effects on the binding of transcription factors. In this study, we present agReg-SNPdb-Plants, a database storing genome-wide collections of regulatory SNPs for agricultural plant species which can be queried via a web interface. Abstract Single nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs can reveal the biologically causative variant and decipher the regulatory mechanisms behind a phenotype. In our previous work, we presented agReg-SNPdb, a database of regulatory SNPs for agriculturally important animal species. To complement this previous work, in this study we present the extension agReg-SNPdb-Plants storing rSNPs and their predicted effects on TF-binding for 13 agriculturally important plant species and subspecies (Brassica napus, Helianthus annuus, Hordeum vulgare, Oryza glaberrima, Oryza glumipatula, Oryza sativa Indica, Oryza sativa Japonica, Solanum lycopersicum, Sorghum bicolor, Triticum aestivum, Triticum turgidum, Vitis vinifera, and Zea mays). agReg-SNPdb-Plants can be queried via a web interface that allows users to search for SNP IDs, chromosomal regions, or genes. For a comprehensive interpretation of GWAS results or larger SNP-sets, it is possible to download the whole list of SNPs and their impact on transcription factor binding sites (TFBSs) from the website chromosome-wise.
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Affiliation(s)
- Selina Klees
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.H.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Carl-Sprengel-Weg 1, Georg-August University, 37075 Göttingen, Germany
- Correspondence: (S.K.); (M.G.)
| | - Felix Heinrich
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.H.); (A.O.S.)
| | - Armin Otto Schmitt
- Breeding Informatics Group, Department of Animal Sciences, Georg-August University, Margarethe von Wrangell-Weg 7, 37075 Göttingen, Germany; (F.H.); (A.O.S.)
- Center for Integrated Breeding Research (CiBreed), Carl-Sprengel-Weg 1, Georg-August University, 37075 Göttingen, Germany
| | - Mehmet Gültas
- Center for Integrated Breeding Research (CiBreed), Carl-Sprengel-Weg 1, Georg-August University, 37075 Göttingen, Germany
- Faculty of Agriculture, South Westphalia University of Applied Sciences, Lübecker Ring 2, 59494 Soest, Germany
- Correspondence: (S.K.); (M.G.)
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Mauki DH, Tijjani A, Ma C, Ng’ang’a SI, Mark AI, Sanke OJ, Abdussamad AM, Olaogun SC, Ibrahim J, Dawuda PM, Mangbon GF, Kazwala RR, Gwakisa PS, Yin TT, Li Y, Peng MS, Adeola AC, Zhang YP. Genome-wide investigations reveal the population structure and selection signatures of Nigerian cattle adaptation in the sub-Saharan tropics. BMC Genomics 2022; 23:306. [PMID: 35428239 PMCID: PMC9012019 DOI: 10.1186/s12864-022-08512-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/29/2022] [Indexed: 11/11/2022] Open
Abstract
Background Cattle are considered to be the most desirable livestock by small scale farmers. In Africa, although comprehensive genomic studies have been carried out on cattle, the genetic variations in indigenous cattle from Nigeria have not been fully explored. In this study, genome-wide analysis based on genotyping-by-sequencing (GBS) of 193 Nigerian cattle was used to reveal new insights on the history of West African cattle and their adaptation to the tropical African environment, particularly in sub-Saharan region. Results The GBS data were evaluated against whole-genome sequencing (WGS) data and high rate of variant concordance between the two platforms was evident with high correlated genetic distance matrices genotyped by both methods suggestive of the reliability of GBS applicability in population genetics. The genetic structure of Nigerian cattle was observed to be homogenous and unique from other African cattle populations. Selection analysis for the genomic regions harboring imprints of adaptation revealed genes associated with immune responses, growth and reproduction, efficiency of feeds utilization, and heat tolerance. Our findings depict potential convergent adaptation between African cattle, dogs and humans with adaptive genes SPRY2 and ITGB1BP1 possibly involved in common physiological activities. Conclusion The study presents unique genetic patterns of Nigerian cattle which provide new insights on the history of cattle in West Africa based on their population structure and the possibility of parallel adaptation between African cattle, dogs and humans in Africa which require further investigations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08512-w.
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Huo B, Liu X, Chen S, Liu J, Zhou Q, Shen J, Li D, Tang R, Chen J, Zhou X. Population Structure, Genetic Diversity and Differentiation of Triplophysa tenuis in Xinjiang Tarim River. Front Genet 2022; 13:860678. [PMID: 35309126 PMCID: PMC8927061 DOI: 10.3389/fgene.2022.860678] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/17/2022] [Indexed: 11/28/2022] Open
Abstract
Triplophysa tenuis is an important indigenous fish in the Xinjiang Tarim River. In this study, we collected 120 T. tenuis individuals from 8 T. tenuis populations in the Tarim River. Through genotyping-by-sequencing (GBS), a total of 582,678,756 clean reads were generated for all the genotypes, and after quality filtering, 595,379 SNPs were obtained for the population genetic analyses. Multiple genetic parameters showed that the 8 T. tenuis populations had high genetic diversity. Phylogenetic tree analysis indicated that all T. tenuis individuals were divided into five branches, the individuals from the north of Tarim River were grouped into cluster 1 (SF and WS) and cluster 3 (DWQ, TKX, and KZE), while the AETS, WLWT and LF individuals from the south of Tarim River were clustered into cluster 2. The result was consistent with the admixture analysis, which supported that the 8 T. tenuis populations were clustered into three subgroups. Furthermore, the pairwise FST values and genetic distance indicated that there was a large genetic differentiation between WS and other T. tenuis populations. Collectively, this study provides valuable genome-wide data for the conservation of natural T. tenuis populations in the Tarim River.
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Affiliation(s)
- Bin Huo
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Xuan Liu
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Shengao Chen
- College of Animal Science, Tarim University, Alar, China
| | - Jieya Liu
- College of Animal Science, Tarim University, Alar, China
| | - Qiong Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jianzhong Shen
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Dapeng Li
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Rong Tang
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
| | - Jing Chen
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Jing Chen, ; Xiaoyun Zhou,
| | - Xiaoyun Zhou
- College of Fisheries, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Jing Chen, ; Xiaoyun Zhou,
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23
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Ayalew H, Anderson JD, Krom N, Tang Y, Butler TJ, Rawat N, Tiwari V, Ma XF. Genotyping-by-sequencing and genomic selection applications in hexaploid triticale. G3 GENES|GENOMES|GENETICS 2022; 12:6460330. [PMID: 34897452 PMCID: PMC9210314 DOI: 10.1093/g3journal/jkab413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/24/2021] [Indexed: 12/02/2022]
Abstract
Triticale, a hybrid species between wheat and rye, is one of the newest additions to the plant kingdom with a very short history of improvement. It has very limited genomic resources because of its large and complex genome. Objectives of this study were to generate dense marker data, understand genetic diversity, population structure, linkage disequilibrium (LD), and estimate accuracies of commonly used genomic selection (GS) models on forage yield of triticale. Genotyping-by-sequencing (GBS), using PstI and MspI restriction enzymes for reducing genome complexity, was performed on a triticale diversity panel (n = 289). After filtering for biallelic loci with more than 70% genome coverage, and minor allele frequency (MAF) > 0.05, de novo variant calling identified 16,378 single nucleotide polymorphism (SNP) markers. Sequences of these variants were mapped to wheat and rye reference genomes to infer their homologous groups and chromosome positions. About 45% (7430), and 58% (9500) of the de novo identified SNPs were mapped to the wheat and rye reference genomes, respectively. Interestingly, 28.9% (2151) of the 7430 SNPs were mapped to the D genome of hexaploid wheat, indicating substantial substitution of the R genome with D genome in cultivated triticale. About 27% of marker pairs were in significant LD with an average r2 > 0.18 (P < 0.05). Genome-wide LD declined rapidly to r2 < 0.1 beyond 10 kb physical distance. The three sub-genomes (A, B, and R) showed comparable LD decay patterns. Genetic diversity and population structure analyses identified five distinct clusters. Genotype grouping did not follow prior winter vs spring-type classification. However, one of the clusters was largely dominated by winter triticale. GS accuracies were estimated for forage yield using three commonly used models with different training population sizes and marker densities. GS accuracy increased with increasing training population size while gain in accuracy tended to plateau with marker densities of 2000 SNPs or more. Average GS accuracy was about 0.52, indicating the potential of using GS in triticale forage yield improvement.
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Affiliation(s)
- Habtamu Ayalew
- Noble Research Institute, LLC., Ardmore, OK 73401, USA
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
| | | | - Nick Krom
- Noble Research Institute, LLC., Ardmore, OK 73401, USA
| | - Yuhong Tang
- Noble Research Institute, LLC., Ardmore, OK 73401, USA
| | | | - Nidhi Rawat
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Vijay Tiwari
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Xue-Feng Ma
- Noble Research Institute, LLC., Ardmore, OK 73401, USA
- Forage Genetics International, West Salem, WI 54669, USA
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Zhao Z, Song Q, Bai D, Niu S, He Y, Qiao D, Chen Z, Li C, Luo J, Li F. Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau. BMC PLANT BIOLOGY 2022; 22:55. [PMID: 35086484 PMCID: PMC8793275 DOI: 10.1186/s12870-022-03438-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/12/2022] [Indexed: 05/17/2023]
Abstract
BACKGROUND Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau. RESULTS We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies. CONCLUSIONS The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.
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Affiliation(s)
- Zhifei Zhao
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Qinfei Song
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Dingchen Bai
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Suzhen Niu
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Yingqin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Dahe Qiao
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Zhengwu Chen
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Caiyun Li
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Jing Luo
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Fang Li
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
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Genetic Diversity and Population Structure Analysis of the USDA Olive Germplasm Using Genotyping-By-Sequencing (GBS). Genes (Basel) 2021; 12:genes12122007. [PMID: 34946959 PMCID: PMC8701156 DOI: 10.3390/genes12122007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/10/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
Abstract
Olives are one of the most important fruit and woody oil trees cultivated in many parts of the world. Olive oil is a critical component of the Mediterranean diet due to its importance in heart health. Olives are believed to have been brought to the United States from the Mediterranean countries in the 18th century. Despite the increase in demand and production areas, only a few selected olive varieties are grown in most traditional or new growing regions in the US. By understanding the genetic background, new sources of genetic diversity can be incorporated into the olive breeding programs to develop regionally adapted varieties for the US market. This study aimed to explore the genetic diversity and population structure of 90 olive accessions from the USDA repository along with six popular varieties using genotyping-by-sequencing (GBS)-generated SNP markers. After quality filtering, 54,075 SNP markers were retained for the genetic diversity analysis. The average gene diversity (GD) and polymorphic information content (PIC) values of the SNPs were 0.244 and 0.206, respectively, indicating a moderate genetic diversity for the US olive germplasm evaluated in this study. The structure analysis showed that the USDA collection was distributed across seven subpopulations; 63% of the accessions were grouped into an identifiable subpopulation. The phylogenetic and principal coordinate analysis (PCoA) showed that the subpopulations did not align with the geographical origins or climatic zones. An analysis of the molecular variance revealed that the major genetic variation sources were within populations. These findings provide critical information for future olive breeding programs to select genetically distant parents and facilitate future gene identification using genome-wide association studies (GWAS) or a marker-assisted selection (MAS) to develop varieties suited to production in the US.
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Guo Z, Yang Q, Huang F, Zheng H, Sang Z, Xu Y, Zhang C, Wu K, Tao J, Prasanna BM, Olsen MS, Wang Y, Zhang J, Xu Y. Development of high-resolution multiple-SNP arrays for genetic analyses and molecular breeding through genotyping by target sequencing and liquid chip. PLANT COMMUNICATIONS 2021; 2:100230. [PMID: 34778746 PMCID: PMC8577115 DOI: 10.1016/j.xplc.2021.100230] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/05/2021] [Accepted: 08/06/2021] [Indexed: 05/26/2023]
Abstract
Genotyping platforms, as critical supports for genomics, genetics, and molecular breeding, have been well implemented at national institutions/universities in developed countries and multinational seed companies that possess high-throughput, automatic, large-scale, and shared facilities. In this study, we integrated an improved genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology to develop a multiple single-nucleotide polymorphism (mSNP) approach in which mSNPs can be captured from a single amplicon. From one 40K maize mSNP panel, we developed three types of markers (40K mSNPs, 251K SNPs, and 690K haplotypes), and generated multiple panels with various marker densities (1K-40K mSNPs) by sequencing at different depths. Comparative genetic diversity analysis was performed with genic versus intergenic markers and di-allelic SNPs versus non-typical SNPs. Compared with the one-amplicon-one-SNP system, mSNPs and within-mSNP haplotypes are more powerful for genetic diversity detection, linkage disequilibrium decay analysis, and genome-wide association studies. The technologies, protocols, and application scenarios developed for maize in this study will serve as a model for the development of mSNP arrays and highly efficient GBTS systems in animals, plants, and microorganisms.
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Affiliation(s)
- Zifeng Guo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Quannv Yang
- School of Food Science and Engineering, Foshan University/CIMMYT-China Tropical Maize Research Center, Foshan 528225, Guangdong, China
| | - Feifei Huang
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang 050035, China
| | - Hongjian Zheng
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences/CIMMYT-China Specialty Maize Research Center, Shanghai 201403, China
| | - Zhiqin Sang
- Xinjiang Academy of Agricultural Reclamation, Shihezi 832000, Xinjiang, China
| | - Yanfen Xu
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang 050035, China
| | - Cong Zhang
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang 050035, China
| | - Kunsheng Wu
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang 050035, China
| | - Jiajun Tao
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang 050035, China
| | - Boddupalli M. Prasanna
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Michael S. Olsen
- CIMMYT (International Maize and Wheat Improvement Center), ICRAF Campus, United Nations Avenue, Nairobi, Kenya
| | - Yunbo Wang
- School of Food Science and Engineering, Foshan University/CIMMYT-China Tropical Maize Research Center, Foshan 528225, Guangdong, China
| | - Jianan Zhang
- MolBreeding Biotechnology Co., Ltd., Shijiazhuang 050035, China
- National Foxtail Millet Improvement Center, Minor Cereal Crops Laboratory of Hebei Province, Institute of Millet Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang 050035, China
| | - Yunbi Xu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- School of Food Science and Engineering, Foshan University/CIMMYT-China Tropical Maize Research Center, Foshan 528225, Guangdong, China
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences/CIMMYT-China Specialty Maize Research Center, Shanghai 201403, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan Texcoco 56130, Mexico
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Plant Variety Protection: Current Practices and Insights. Genes (Basel) 2021; 12:genes12081127. [PMID: 34440301 PMCID: PMC8392850 DOI: 10.3390/genes12081127] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Breeders persistently supply farmers with the best varieties in order to exceed consumer demand through plant-breeding processes that are resource-intensive. In order to motivate continuous innovation in variety development, a system needs to provide incentives for plant breeders to develop superior varieties, for example, exclusive ownership to produce and market those varieties. The most common system is the acquisition of intellectual property protection through plant variety protection, also known as the breeder’s right. Most countries have adopted the system established by the International Union for the Protection of New Varieties of Plants (UPOV). To be granted plant variety protection, the variety should prove to be unique by meeting three requirements: distinctness, uniformity, and stability. This review summarizes (1) the plant variety protection via UPOV convention, (2) technical methods for distinctness, uniformity, and stability testing via phenotype, molecular markers, and sequencing as well as their challenges and potentiality, and (3) additional discussions in essentially derived variety, value for cultivation and use testing, and open source seed initiative.
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Cao S, Song J, Yuan Y, Zhang A, Ren J, Liu Y, Qu J, Hu G, Zhang J, Wang C, Cao J, Olsen M, Prasanna BM, San Vicente F, Zhang X. Genomic Prediction of Resistance to Tar Spot Complex of Maize in Multiple Populations Using Genotyping-by-Sequencing SNPs. FRONTIERS IN PLANT SCIENCE 2021; 12:672525. [PMID: 34335648 PMCID: PMC8322742 DOI: 10.3389/fpls.2021.672525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Tar spot complex (TSC) is one of the most important foliar diseases in tropical maize. TSC resistance could be furtherly improved by implementing marker-assisted selection (MAS) and genomic selection (GS) individually, or by implementing them stepwise. Implementation of GS requires a profound understanding of factors affecting genomic prediction accuracy. In the present study, an association-mapping panel and three doubled haploid populations, genotyped with genotyping-by-sequencing, were used to estimate the effectiveness of GS for improving TSC resistance. When the training and prediction sets were independent, moderate-to-high prediction accuracies were achieved across populations by using the training sets with broader genetic diversity, or in pairwise populations having closer genetic relationships. A collection of inbred lines with broader genetic diversity could be used as a permanent training set for TSC improvement, which can be updated by adding more phenotyped lines having closer genetic relationships with the prediction set. The prediction accuracies estimated with a few significantly associated SNPs were moderate-to-high, and continuously increased as more significantly associated SNPs were included. It confirmed that TSC resistance could be furtherly improved by implementing GS for selecting multiple stable genomic regions simultaneously, or by implementing MAS and GS stepwise. The factors of marker density, marker quality, and heterozygosity rate of samples had minor effects on the estimation of the genomic prediction accuracy. The training set size, the genetic relationship between training and prediction sets, phenotypic and genotypic diversity of the training sets, and incorporating known trait-marker associations played more important roles in improving prediction accuracy. The result of the present study provides insight into less complex trait improvement via GS in maize.
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Affiliation(s)
- Shiliang Cao
- Maize Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Junqiao Song
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
- College of Agronomy, Henan University of Science and Technology, Luoyang, China
- Maize Research Institute, Anyang Academy of Agricultural Sciences, Anyang, China
| | - Yibing Yuan
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Ao Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Jiaojiao Ren
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
| | - Yubo Liu
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang, China
| | - Jingtao Qu
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guanghui Hu
- Maize Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Jianguo Zhang
- Maize Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Chunping Wang
- Maize Research Institute, Anyang Academy of Agricultural Sciences, Anyang, China
| | - Jingsheng Cao
- Maize Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Michael Olsen
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Felix San Vicente
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico
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Ramírez‐Reyes T, Flores‐Villela O, Piñero D, Lathrop A, Murphy RW. Genomic assessment of the
Phyllodactylus tuberculosus
complex (Reptilia: Phyllodactylidae) in America. ZOOL SCR 2021. [DOI: 10.1111/zsc.12492] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tonatiuh Ramírez‐Reyes
- Posgrado en Ciencias Biológicas Universidad Nacional Autónoma de México México City México
- Museo de Zoología Facultad de Ciencias Universidad Nacional Autónoma de Méxic México City México
- Departamento de Ecología Evolutiva Instituto de EcologíaUniversidad Nacional Autónoma de México México City México
| | - Oscar Flores‐Villela
- Museo de Zoología Facultad de Ciencias Universidad Nacional Autónoma de Méxic México City México
| | - Daniel Piñero
- Departamento de Ecología Evolutiva Instituto de EcologíaUniversidad Nacional Autónoma de México México City México
| | - Amy Lathrop
- Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada
| | - Robert W. Murphy
- Centre for Biodiversity and Conservation Biology Royal Ontario Museum Toronto ON Canada
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Ren J, Li Z, Wu P, Zhang A, Liu Y, Hu G, Cao S, Qu J, Dhliwayo T, Zheng H, Olsen M, Prasanna BM, San Vicente F, Zhang X. Genetic Dissection of Quantitative Resistance to Common Rust ( Puccinia sorghi) in Tropical Maize ( Zea mays L.) by Combined Genome-Wide Association Study, Linkage Mapping, and Genomic Prediction. FRONTIERS IN PLANT SCIENCE 2021; 12:692205. [PMID: 34276741 PMCID: PMC8284423 DOI: 10.3389/fpls.2021.692205] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/08/2021] [Indexed: 05/03/2023]
Abstract
Common rust is one of the major foliar diseases in maize, leading to significant grain yield losses and poor grain quality. To dissect the genetic architecture of common rust resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid (DH) population, DH1, were used to perform GWAS and linkage mapping analyses. The GWAS results revealed six single-nucleotide polymorphisms (SNPs) significantly associated with quantitative resistance of common rust at a very stringent threshold of P-value 3.70 × 10-6 at bins 1.05, 1.10, 3.04, 3.05, 4.08, and 10.04. Linkage mapping identified five quantitative trait loci (QTL) at bins 1.03, 2.06, 4.08, 7.03, and 9.00. The phenotypic variation explained (PVE) value of each QTL ranged from 5.40 to 12.45%, accounting for the total PVE value of 40.67%. Joint GWAS and linkage mapping analyses identified a stable genomic region located at bin 4.08. Five significant SNPs were only identified by GWAS, and four QTL were only detected by linkage mapping. The significantly associated SNP of S10_95231291 detected in the GWAS analysis was first reported. The linkage mapping analysis detected two new QTL on chromosomes 7 and 10. The major QTL on chromosome 7 in the region between 144,567,253 and 149,717,562 bp had the largest PVE value of 12.45%. Four candidate genes of GRMZM2G328500, GRMZM2G162250, GRMZM2G114893, and GRMZM2G138949 were identified, which played important roles in the response of stress resilience and the regulation of plant growth and development. Genomic prediction (GP) accuracies observed in the GWAS panel and DH1 population were 0.61 and 0.51, respectively. This study provided new insight into the genetic architecture of quantitative resistance of common rust. In tropical maize, common rust could be improved by pyramiding the new sources of quantitative resistance through marker-assisted selection (MAS) or genomic selection (GS), rather than the implementation of MAS for the single dominant race-specific resistance gene.
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Affiliation(s)
- Jiaojiao Ren
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Zhimin Li
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Penghao Wu
- College of Agronomy, Xinjiang Agricultural University, Urumqi, China
| | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, China
| | - Yubo Liu
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Guanghui Hu
- Maize Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Shiliang Cao
- Maize Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Jingtao Qu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Thanda Dhliwayo
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Hongjian Zheng
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Michael Olsen
- International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
| | | | - Felix San Vicente
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- *Correspondence: Felix San Vicente,
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
- Xuecai Zhang,
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