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Flores-Saavedra M, Plazas M, Gramazio P, Vicente O, Vilanova S, Prohens J. Growth and antioxidant responses to water stress in eggplant MAGIC population parents, F 1 hybrids and a subset of recombinant inbred lines. BMC PLANT BIOLOGY 2024; 24:560. [PMID: 38877388 PMCID: PMC11179202 DOI: 10.1186/s12870-024-05235-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
BACKGROUND The generation of new eggplant (Solanum melongena L.) cultivars with drought tolerance is a main challenge in the current context of climate change. In this study, the eight parents (seven of S. melongena and one of the wild relative S. incanum L.) of the first eggplant MAGIC (Multiparent Advanced Generation Intercrossing) population, together with four F1 hybrids amongst them, five S5 MAGIC recombinant inbred lines selected for their genetic diversity, and one commercial hybrid were evaluated in young plant stage under water stress conditions (30% field capacity; FC) and control conditions (100% FC). After a 21-day treatment period, growth and biomass traits, photosynthetic pigments, oxidative stress markers, antioxidant compounds, and proline content were evaluated. RESULTS Significant effects (p < 0.05) were observed for genotype, water treatments and their interaction in most of the traits analyzed. The eight MAGIC population parental genotypes displayed a wide variation in their responses to water stress, with some of them exhibiting enhanced root development and reduced foliar biomass. The commercial hybrid had greater aerial growth compared to root growth. The four F1 hybrids among MAGIC parents differed in their performance, with some having significant positive or negative heterosis in several traits. The subset of five MAGIC lines displayed a wide diversity in their response to water stress. CONCLUSION The results show that a large diversity for tolerance to drought is available among the eggplant MAGIC materials, which can contribute to developing drought-tolerant eggplant cultivars.
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Affiliation(s)
- Martín Flores-Saavedra
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain.
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | - Oscar Vicente
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, Valencia, 46022, Spain
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Chen X, Huang L, Fan J, Yan S, Zhou G, Zhang J. KASP-IEva: an intelligent typing evaluation model for KASP primers. FRONTIERS IN PLANT SCIENCE 2024; 14:1293599. [PMID: 38510833 PMCID: PMC10952001 DOI: 10.3389/fpls.2023.1293599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/27/2023] [Indexed: 03/22/2024]
Abstract
KASP marker technology has been used in molecular marker-assisted breeding because of its high efficiency and flexibility, and an intelligent evaluation model of KASP marker primer typing results is essential to improve the efficiency of marker development on a large scale. To this end, this paper proposes a gene population delineation method based on NTC identification module and data distribution judgment module to improve the accuracy of K-Means clustering, and introduces a decision tree to construct the KASP-IEva primer typing evaluation model. The model firstly designs the NTC identification module and data distribution judgment module to extract four types of data, grouping and categorizing to achieve the improvement of the distinguishability of amplification product signals; secondly, the K-Means algorithm is used to aggregate and classify the data, to visualize the five aggregated clusters and to obtain the morphology location eigenvalues; lastly, the evaluation criteria for the typing effect level are constructed, and the logical decision tree is used to make conditional discrimination on the eigenvalues in order to realize the score prediction. The performance of the model was tested by the KASP marker typing test results of 2519 groups of cotton varieties, and the following conclusions were obtained: the model is able to visualize the aggregation and classification effects of the amplification products of NTC, pure genotypes, heterozygous genotypes, and untyped genotypes, enabling rapid and accurate KASP marker typing evaluation. Comparing and analyzing the model evaluation results with the expert evaluation results, the average accuracy rate of the four grades evaluated by the model was 87%, and the overall evaluation results showed an uneven distribution of the grades with significant differential characteristics. When evaluating 2519 KASP fractal maps, the expert evaluation consumes 15 hours, and the model evaluation only uses 8min27.45s, which makes the model intelligent evaluation significantly better than the expert evaluation from the perspective of time. The establishment of the model will further enhance the application of KASP markers in molecular marker-assisted breeding and provide technical support for the large-scale screening and identification of excellent genotypes.
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Affiliation(s)
- Xiaojing Chen
- National Agriculture Science Data Center, Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Longyu Huang
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Jingchao Fan
- National Agriculture Science Data Center, Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
| | - Shen Yan
- National Agriculture Science Data Center, Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guomin Zhou
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jianhua Zhang
- National Agriculture Science Data Center, Agricultural Information Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Nanfan Research Institute, Chinese Academy of Agricultural Sciences, Sanya, China
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Liu Y, Kim HJ. Attenuated Total Reflection Fourier Transform Infrared Spectroscopy with Soft Independent Modeling of Class Analogy-Principal Component Analysis for Classifying Cotton Fiber Maturity Phenotypes of Cotton Population Composed of Various Genotypes. APPLIED SPECTROSCOPY 2024; 78:99-110. [PMID: 37933119 DOI: 10.1177/00037028231211942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Maturity is a major fiber trait that affects the processing and performance of cotton fiber. Rapid and accurate identification of fiber maturity phenotypes and genotypes is of importance to breeders. Previous studies showed that either conventional fiber measurements or attenuated total reflection Fourier transform infrared spectroscopy (ATR FT-IR) analysis discriminated the immature fiber (im) phenotype from the wild type (WT) mature fiber phenotype in a segregating F2 population from a cross between two upland cotton lines differing in fiber maturity. However, both conventional fiber property measurement methods and FT-IR analyses with current algorithms could not detect the subtle differences among the WT fibers composed of two different genotypes, WT homozygosity (WT-homo) and WT heterozygosity (WT-hetero). This research explored the FT-IR method, in combination with soft independent modeling of class analogy of principal component analysis (SIMCA-PCA), for the discrimination of WT fiber phenotypes consisting of two different genotypes (WT-homo and WT-hetero). The new approach enabled the detection of IR spectral intensity differences between WT-homo and WT-hetero fibers. Successful classification originated from a distinctive spectral difference in the low-wavenumber region (<700 cm-1) between WT-hetero fibers and WT-homo fibers. This observation emphasized that ATR FT-IR with a SIMCA-PCA approach would be a sensitive tool for classifying the WT fibers demonstrating minor phenotypic differences. The improved sensitivity of the infrared method may provide a way of dissecting genotype-phenotype interactions of cotton fibers rapidly and efficiently.
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Affiliation(s)
- Yongliang Liu
- USDA, ARS, Southern Regional Research Center, Cotton Structure and Quality Research Unit, New Orleans, Louisiana, USA
| | - Hee-Jin Kim
- USDA, ARS, Southern Regional Research Center, Cotton Fiber Bioscience Research Unit, New Orleans, Louisiana, USA
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4
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Li R, Tian M, He Q, Zhang L. Correlation between Parental Transcriptome and Field Data for the Characterization of Heterosis in Chinese Cabbage. Genes (Basel) 2023; 14:genes14040776. [PMID: 37107533 PMCID: PMC10137735 DOI: 10.3390/genes14040776] [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: 01/02/2023] [Revised: 02/20/2023] [Accepted: 03/20/2023] [Indexed: 04/29/2023] Open
Abstract
In Chinese cabbage breeding, hybrids have made a terrific contribution due to heterosis, the superior performance of offspring compared to their inbred parents. Since the development of new, top-performing hybrids requires a large scale of human and material resources, the prediction of hybrid performance is of utmost interest to plant breeders. In our research, leaf transcriptome data from eight parents were used to investigate if they might be employed as markers to predict hybrid performance and heterosis. In Chinese cabbage, heterosis of plant growth weight (PGW) and heterosis of head weight (HW) were more obvious than other traits. The number of differential expression genes (DEGs) between parents was related to the PGW, length of the biggest outer leaf (LOL), leaf head height (LHH), leaf head width (LHW), HW, leaf number of head (LNH) and plant height (PH) of hybrids, and up-regulated DEGs number was also associated with these traits. Euclidean and binary distances of parental gene expression levels were significantly correlated with the PGW, LOL, LHH, LHW, HW and PH of hybrids. Additionally, there was a significant correlation between the parental expression levels of multiple genes involved in the ribosomal metabolic pathway and hybrid observations and heterosis in PGW, with the BrRPL23A gene showing the highest correlation with the MPH of PGW(r = 0.75). Therefore, leaf transcriptome data can preliminarily predict the hybrid performance and select parents in Chinese cabbage.
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Affiliation(s)
- Ru Li
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Min Tian
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Qiong He
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Lugang Zhang
- State Key Laboratory of Crop Stress Biology for Arid Area, College of Horticulture, Northwest A&F University, Yangling 712100, China
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Abdel-Aty MS, Sorour FA, Yehia WMB, Kotb HMK, Abdelghany AM, Lamlom SF, Shah AN, Abdelsalam NR. Estimating the combining ability and genetic parameters for growth habit, yield, and fiber quality traits in some Egyptian cotton crosses. BMC PLANT BIOLOGY 2023; 23:121. [PMID: 36859186 PMCID: PMC9979479 DOI: 10.1186/s12870-023-04131-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
It is crucial to understand how targeted traits in a hybrid breeding program are influenced by gene activity and combining ability. During the three growing seasons of 2015, 2016, and 2017, a field study was conducted with twelve cotton genotypes, comprised of four testers and eight lines. Thirty-two F1 crosses were produced in the 2015 breeding season using the line x tester mating design. The twelve genotypes and their thirty-two F1 crosses were then evaluated in 2016 and 2017. The results demonstrated highly significant differences among cotton genotypes for all the studied traits, showing a wide range of genetic diversity in the parent genotypes. Additionally, the line-x-tester interaction was highly significant for all traits, suggesting the impact of both additive and non-additive variations in gene expression. Furthermore, the thirty-two cotton crosses showed high seed cotton output, lint cotton yield, and fiber quality, such as fiber length values exceeding 31 mm and a fiber strength above 10 g/tex. Accordingly, selecting lines and testers with high GCA effects and crosses with high SCA effects would be an effective approach to improve the desired traits in cotton and develop new varieties with excellent yield and fiber quality.
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Affiliation(s)
- M S Abdel-Aty
- Agronomy Department, Faculty of Agriculture, Kafr El-Sheikh University, Kafr El-Sheikh, 33516, Egypt
| | - F A Sorour
- Agronomy Department, Faculty of Agriculture, Kafr El-Sheikh University, Kafr El-Sheikh, 33516, Egypt
| | - W M B Yehia
- Cotton Breeding Department, Cotton Research Institute, Agriculture Research Center, Giza, Egypt
| | - H M K Kotb
- Cotton Breeding Department, Cotton Research Institute, Agriculture Research Center, Giza, Egypt
| | - Ahmed M Abdelghany
- Crop Science Department, Faculty of Agriculture, Damanhour University, Damanhour, 22516, Egypt
| | - Sobhi F Lamlom
- Plant Production Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Punjab, 64200, Pakistan.
| | - Nader R Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, 21531, Egypt.
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Jiang F, Yin X, Li ZW, Guo R, Wang J, Fan J, Zhang Y, Kang MS, Fan X. Predicting heterosis via genetic distance and the number of SNPs in selected segments of chromosomes in maize. FRONTIERS IN PLANT SCIENCE 2023; 14:1111961. [PMID: 36875600 PMCID: PMC9982102 DOI: 10.3389/fpls.2023.1111961] [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: 11/30/2022] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
A reliable method is needed for predicting heterosis to help maize (Zea mays L.) breeders develop new hybrids more efficiently. The objectives of this study were to 1) investigate if the numbers of selected PEUS SNPs (the SNP in the Promoters (1 kb upstream of the start codon), Exons, Untranslated region (UTR), and Stop codons) could be used for predicting MPH or BPH of GY; 2) if the number of PEUS SNPs is a better predictor of MPH and/or BPH of GY than genetic distance (GD). A line × tester experiment was conducted with 19 elite maize inbreds from three heterotic groups, which were crossed with five testers. The multi-location trial data on GY were recorded. Whole-genome resequencing of the 24 inbreds was carried out. After filtration, a total of 58,986,791 SNPs were called with high confidence. Selected SNPs in the promoters, exons, untranslated region (UTRs), and stop codons (PEUS SNPs) were counted, and the GD was calculated. The correlation between heterozygous PEUS SNPs/GD and mean MPH, BPH of GY revealed that 1) both the number of heterozygous PEUS SNP and the GD were highly correlated to both MPH_GY and BPH_GY at p<0.01 with correlation coefficients for the number of heterozygous PEUS SNP being higher than that for GD; 2) the mean number of heterozygous PEUS SNPs was also highly correlated with mean BPH_GY or mean MPH_GY (p<0.05) in the 95 crosses grouped by either male or female parents, implying that inbreds can be selected before making the actual crosses in the field. We concluded that the number of heterozygous PEUS SNPs would be a better predictor of MPH_GY and BPH_GY than GD. Hence, maize breeders could use heterozygous PEUS SNPs to select inbreds with high heterosis potential before actually making the crosses, thus improving the breeding efficiency.
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Affiliation(s)
- Fuyan Jiang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, Yunnan, China
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - XingFu Yin
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Zi Wei Li
- Yunnan Dehong Dai and Jingpo Nationality Institute of Agricultural Sciences, Mangshi, Yunnan, China
| | - Ruijia Guo
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Jing Wang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Jun Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Yudong Zhang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
| | - Manjit S. Kang
- Department of Plant Pathology, Kansas State University, Manhattan, KS, United States
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China
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González-Orenga S, Plazas M, Ribera E, Pallotti C, Boscaiu M, Prohens J, Vicente O, Fita A. Transgressive Biochemical Response to Water Stress in Interspecific Eggplant Hybrids. PLANTS (BASEL, SWITZERLAND) 2023; 12:194. [PMID: 36616323 PMCID: PMC9824389 DOI: 10.3390/plants12010194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/24/2022] [Accepted: 12/28/2022] [Indexed: 06/17/2023]
Abstract
In a climate change scenario, crop tolerance to drought must be urgently improved, as it represents an increasingly critical stress reducing agricultural yields worldwide. Although most crops are relatively sensitive to water stress, many of their wild relatives are more tolerant and may be used to improve drought tolerance in our crops. In this study, the response to drought of eggplant (Solanum melongena), its close wild relatives S. insanum and S. incanum and their interspecific hybrids with S. melongena was assessed. The plants were subjected to two treatments for 18 days: control, with irrigation every four days, and drought, with complete interruption of irrigation. Morphological and biomass traits were measured, and physiological and biochemical responses were analysed using stress biomarkers such as proline, flavonoids, and total phenolic compounds. Oxidative stress was quantified by measuring malondialdehyde (MDA) content. As a result of the drought treatment, plant development and tissue water content were seriously affected. Generally, water deficit also caused significant increases in MDA, proline, flavonoids, and total phenolics compounds. Our results comparing parental accessions reveal a better response to drought in one of the S. insanum accessions. The hybrid between S. melongena and S. incanum displayed a better response than the other hybrids and even its parents. The results obtained here might be helpful for future eggplant breeding programmes aimed at improving drought tolerance.
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Affiliation(s)
- Sara González-Orenga
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
- Department of Plant Biology and Soil Science, Faculty of Biology, Universidad de Vigo, Campus Lagoas-Marcosendre, 36310 Vigo, Spain
| | - Mariola Plazas
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Elvira Ribera
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Claudia Pallotti
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Monica Boscaiu
- Mediterranean Agroforestry Institute (IAM), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Jaime Prohens
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Oscar Vicente
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Ana Fita
- Institute for the Conservation and Improvement of Valencian Agrodiversity (COMAV), Universitat Politècnica de València, Camino de Vera s/n, 46022 Valencia, Spain
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Ibrar D, Khan S, Mahmood T, Bakhsh A, Aziz I, Rais A, Ahmad R, Bashir S, Nawaz M, Rashid N, Irshad S, Alotaibi SS, Dvorackova H, Dvoracek J, Hasnain Z. Molecular markers-based DNA fingerprinting coupled with morphological diversity analysis for prediction of heterotic grouping in sunflower ( Helianthus annuus L.). FRONTIERS IN PLANT SCIENCE 2022; 13:916845. [PMID: 35968099 PMCID: PMC9366523 DOI: 10.3389/fpls.2022.916845] [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: 04/10/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Cultivated sunflower holds a very narrow genetic base and the efficient utilization of available genetic diversity is very important for a successful breeding program. In the present study, 109 sunflower genotypes were assessed for diversity paneling through a combined approach of morphological and molecular markers analysis. Morphological parameters including days to flower initiation, days to flower completion, plant height, stem curvature, number of leaves per plant, leaf area, head diameter, hundred seed weight, and seed yield per plant were studied. Simple sequence repeats (40 DNA markers) were deployed for diversity profiling. Data were analyzed by both univariate and multivariate statistics. SD and coefficient of variation confirm the presence of significant amounts of genetic variation for all the morphological parameters. Cluster Analysis and Principal Component Analysis further confirm the presence of distinct grouping patterns in the studied material. Cluster analysis of both morphological and molecular analysis revealed that restorer lines tend to group separately from A, B, and open-pollinated lines. Further grouping, at the sub-cluster level, revealed six distinct sub-clusters in each of the two major clusters. In total, 12 genotypes, 6 CMS lines (CMS-HAP-12, CMS-HAP-54, CMS-HAP-56, CMS-HAP-99, CMS-HAP-111, and CMS-HAP-112) and 6 restorer lines (RHP-38, RHP-41, RHP-53, RHP-68, RHP-69, and RHP-71) could be used as potential parents for hybrid development. As genotypes of similar genetic backgrounds tend to group closer, it is deduced that one genotype with the highest seed yield per plant could be used for further hybrid breeding programs in sunflowers.
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Affiliation(s)
- Danish Ibrar
- National Agricultural Research Centre, Islamabad, Pakistan
- Department of Plant Breeding and Genetics, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - Shahbaz Khan
- National Agricultural Research Centre, Islamabad, Pakistan
| | - Talat Mahmood
- Department of Plant Breeding and Genetics, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
| | - Ali Bakhsh
- Department of Plant Breeding and Genetics, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Irum Aziz
- Department of Plant Breeding and Genetics, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Afroz Rais
- Department of Botany, Sardar Bahadur Khan Women's University, Quetta, Pakistan
| | - Rafiq Ahmad
- Barani Agriculture Research Institute, Chakwal, Pakistan
| | - Saqib Bashir
- Department of Soil and Environmental Science, Ghazi University, Dera Ghazi Khan, Pakistan
| | - Muhammad Nawaz
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Nabila Rashid
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Sohail Irshad
- Department of Agronomy, MNS-University of Agriculture, Multan, Pakistan
| | - Saqer S. Alotaibi
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Helena Dvorackova
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | | | - Zuhair Hasnain
- Department of Agronomy, Pir Mehr Ali Shah Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan
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Niu H, Ge Q, Shang H, Yuan Y. Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton. Front Genet 2022; 13:855574. [PMID: 35450216 PMCID: PMC9016478 DOI: 10.3389/fgene.2022.855574] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Cotton (Gossypium spp.) is an important natural fiber plant. Lint percentage (LP) is one of the most important determinants of cotton yield and is a typical quantitative trait with high variation and heritability. Many cotton LP genetic linkages and association maps have been reported. This work summarizes the inheritance, quantitative trait loci (QTLs), and candidate genes of LP to facilitate LP genetic study and molecular breeding. More than 1439 QTLs controlling LP have been reported. Excluding replicate QTLs, 417 unique QTLs have been identified on 26 chromosomes, including 243 QTLs identified at LOD >3. More than 60 are stable, major effective QTLs that can be used in marker-assisted selection (MAS). More than 90 candidate genes for LP have been reported. These genes encode MYB, HOX, NET, and other proteins, and most are preferentially expressed during fiber initiation and elongation. A putative molecular regulatory model of LP was constructed and provides the foundation for the genetic study and molecular breeding of LP.
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Affiliation(s)
- Hao Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Haihong Shang, ; Youlu Yuan,
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10
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Hu Y, Xiong J, Shalby N, Zhuo C, Jia Y, Yang QY, Tu J. Comparison of dynamic 3D chromatin architecture uncovers heterosis for leaf size in Brassica napus. J Adv Res 2022; 42:289-301. [PMID: 36513419 PMCID: PMC9788941 DOI: 10.1016/j.jare.2022.01.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/28/2021] [Accepted: 01/02/2022] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Heterosis is the major event driving plant development and promoting crop breeding, but the molecular bases for this phenomenon remain elusive. OBJECTIVES We aim to explore the effect of three-dimensional (3D) chromatin architecture on the underlying mechanism of heterosis. METHODS Here, we constructed the North Carolina II (NC-II) population to select superior and inferior heterosis sets by comparing mid-parent heterosis (MPH) in Brassica napus. To decipher the impact of 3D chromatin architecture on the underlying mechanism of heterosis, we combined genetics, transcriptomics and 3D genomics approaches. RESULTS We suggest that F1 hybrids with superior heterosis tend to contain more transcriptionally active A compartments compared with F1 hybrids with inferior heterosis, and approximately 19-21% compartment significantly altered in the F1 hybrids relative to the parental lines. Further analyses show that chromatin compartments correlate with genetic variance among parents, which may form the basis for differentially active chromatin compartments. Having more A compartments in F1 hybrids confers a more accessible chromatin circumstance, which promotes a higher proportion of highly expressed ELD (expression level dominance) genes in superior heterosis F1 hybrids (46-64%) compared with inferior heterosis F1 hybrids (22-31%). Moreover, genes related to hormones which affect plant growth, are more up-regulated with changes of 3D genome architecture, and we validate that increased hormone content contributes to cell proliferation and expansion by influencing the key genes of cell cycle thereby promoting leaf size. CONCLUSION Dynamic 3D chromatin architecture correlates with genetic variance among parents and contributes to heterosis in Brassica napus.
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Affiliation(s)
- Yue Hu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - Jie Xiong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Nesma Shalby
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Chenjian Zhuo
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China
| | - Yupeng Jia
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China
| | - Qing-Yong Yang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China,Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, 430070 Wuhan, China,Corresponding authors at: National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China (Q.-Y. Yang).
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China,Corresponding authors at: National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070 Wuhan, China (Q.-Y. Yang).
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Havrlentová M, Ondreičková K, Hozlár P, Gregusová V, Mihálik D, Kraic J. Formation of Potential Heterotic Groups of Oat Using Variation at Microsatellite Loci. PLANTS 2021; 10:plants10112462. [PMID: 34834825 PMCID: PMC8621079 DOI: 10.3390/plants10112462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 01/06/2023]
Abstract
An evaluation of polymorphism at the microsatellite loci was applied in distinguishing 85 oat (Avena sativa L.) genotypes selected from the collection of genetic resources. The set of genotypes included oats with white, yellow, and brown seeds as well as a subgroup of naked oat (Avena sativa var. nuda Koern). Variation at these loci was used to form potential heterotic groups potentially used in the oat breeding program. Seven from 20 analyzed microsatellite loci revealed polymorphism. Altogether, 35 microsatellite alleles were detected (2–10 per locus). Polymorphic patterns completely differentiated all genotypes within the subgroups of white, brown, and naked oats, respectively. Only within the greatest subgroup of yellow genotypes, four pairs of genotypes remained unseparated. Genetic differentiation between the oat subgroups allowed the formation of seven potential heterotic groups using the STRUCTURE analysis. The overall value of the fixation index (Fst) suggested a high genetic differentiation between the subgroups and validated a heterotic grouping. This approach can be implemented as a simple predictor of heterosis in parental crosses prior to extensive field testing or development and implementation of more accurate genomic selection.
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Affiliation(s)
- Michaela Havrlentová
- National Agricultural and Food Center, Research Institute of Plant Production, Bratislavská Cesta 122, 92168 Piešťany, Slovakia; (K.O.); (P.H.); (D.M.); (J.K.)
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie Jozefa Herdu 2, 91701 Trnava, Slovakia;
- Correspondence:
| | - Katarína Ondreičková
- National Agricultural and Food Center, Research Institute of Plant Production, Bratislavská Cesta 122, 92168 Piešťany, Slovakia; (K.O.); (P.H.); (D.M.); (J.K.)
| | - Peter Hozlár
- National Agricultural and Food Center, Research Institute of Plant Production, Bratislavská Cesta 122, 92168 Piešťany, Slovakia; (K.O.); (P.H.); (D.M.); (J.K.)
| | - Veronika Gregusová
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie Jozefa Herdu 2, 91701 Trnava, Slovakia;
| | - Daniel Mihálik
- National Agricultural and Food Center, Research Institute of Plant Production, Bratislavská Cesta 122, 92168 Piešťany, Slovakia; (K.O.); (P.H.); (D.M.); (J.K.)
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie Jozefa Herdu 2, 91701 Trnava, Slovakia;
| | - Ján Kraic
- National Agricultural and Food Center, Research Institute of Plant Production, Bratislavská Cesta 122, 92168 Piešťany, Slovakia; (K.O.); (P.H.); (D.M.); (J.K.)
- Department of Biotechnology, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, Námestie Jozefa Herdu 2, 91701 Trnava, Slovakia;
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Amiteye S. Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon 2021; 7:e08093. [PMID: 34765757 PMCID: PMC8569399 DOI: 10.1016/j.heliyon.2021.e08093] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/27/2022] Open
Abstract
The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR- or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.
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Affiliation(s)
- Samuel Amiteye
- Department of Nuclear Agriculture and Radiation Processing (NARP), Graduate School of Nuclear and Allied Sciences (SNAS), College of Basic and Applied Sciences, University of Ghana, P. O. Box AE 1, Accra, Ghana
- Biotechnology Centre, Biotechnology and Nuclear Agriculture Research Institute (BNARI), Ghana Atomic Energy Commission (GAEC), P. O. Box AE 50, Accra, Ghana
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