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Genetic diversity analysis of Prishniparni, Uraria picta Desv.: A Dashmoola ingredient, to realize high yielding accessions. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00402-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022] Open
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Brake M, Al-Qadumii L, Hamasha H, Migdadi H, Awad A, Haddad N, Sadder MT. Development of SSR Markers Linked to Stress Responsive Genes along Tomato Chromosome 3 (Solanum lycopersicum L.). BIOTECH 2022; 11:biotech11030034. [PMID: 35997342 PMCID: PMC9397033 DOI: 10.3390/biotech11030034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/22/2022] Open
Abstract
This study aimed to develop novel SSR markers in tomato. Several BAC clones along chromosome 3 in tomato were selected based on their content. The criteria was the availability of genes, either directly or indirectly related to stress response (drought, salinity, and heat) in tomato. A total of 20 novel in silico SSR markers were developed and 96 important nearby genes were identified. The identified nearby genes represent different tomato genes involved in plant growth and development and biotic and abiotic stress tolerance. The developed SSR markers were assessed using tomato landraces. A total of 29 determinate and semi-determinate local tomato landraces collected from diverse environments were utilized. A total of 33 alleles with mean of 1.65 alleles per locus were scored, showing 100% polymorphic patterns, with a mean of 0.18 polymorphism information content (PIC) values. The mean of observed and expected heterozygosity were 0.19 and 0.24, respectively. The mean value of the Jaccard similarity index was used for clustering the landraces. The developed microsatellite markers showed potential to assess genetic variability among tomato landraces. The genetic distance information reported in this study can be used by breeders in future genetic improvement of tomato for tolerance against diverse stresses.
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Affiliation(s)
- Mohammad Brake
- Science Department, Jerash University, Jerash 26150, Jordan
| | - Lana Al-Qadumii
- Faculty of Science, Philadelphia University, Jerash 19392, Jordan
| | - Hassan Hamasha
- Science Department, Jerash University, Jerash 26150, Jordan
| | | | - Abi Awad
- Food Testing Lab, Jordan Standards and Metrology Organization, Amman 11194, Jordan
| | - Nizar Haddad
- National Agricultural Research Center, Amman 19381, Jordan
| | - Monther T. Sadder
- Plant Biotechnology Lab, Department of Horticulture and Crop Science, School of Agriculture, University of Jordan, Amman 11942, Jordan
- Correspondence:
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Kumar M, Tomar M, Potkule J, Reetu, Punia S, Dhakane-Lad J, Singh S, Dhumal S, Chandra Pradhan P, Bhushan B, Anitha T, Alajil O, Alhariri A, Amarowicz R, Kennedy JF. Functional characterization of plant-based protein to determine its quality for food applications. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.106986] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Sánchez-Velásquez JJ, Reyes-Flores LE, Yzásiga-Barrera C, Zelada-Mázmela E. Performance comparison of gel and capillary electrophoresis-based microsatellite genotyping strategies in a population research and kinship testing framework. BMC Res Notes 2021; 14:444. [PMID: 34876205 PMCID: PMC8650532 DOI: 10.1186/s13104-021-05861-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 11/26/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The advancement of molecular techniques in an era in which high-throughput sequencing has revolutionized biology renders old-fashioned alternatives to high-throughput methods obsolete. Such advanced molecular techniques, however, are not yet accessible to economically disadvantaged region-based laboratories that still obtain DNA profiles using gel-based techniques. To explore whether cost-efficient techniques can produce results that are as robust as those obtained using high-throughput methods, we compared the performance of polyacrylamide gel electrophoresis (PAGE)- and capillary electrophoresis (CE)-derived genomic data in estimating genetic diversity and inferring relatedness using 70 individuals of fine flounder (Paralichthys adspersus) selected from a hatchery population and genotyped for five microsatellite loci. RESULTS Here, we show that PAGE- and CE-derived genomic datasets yield comparable genetic diversity levels regarding allelic diversity measures and heterozygosity. However, relatedness inferred from each dataset showed that the categorization of dyads in the different relationship categories strongly differed. This suggests that while scientists can reliably use PAGE-derived genomic data to estimate genetic diversity, they cannot use the same for parentage testing. The findings could help laboratories committed to population research not be discouraged from using the PAGE system if high-throughput technologies are unavailable and the method is adequate to address the biological question.
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Affiliation(s)
- Julissa J Sánchez-Velásquez
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences, Universidad Nacional del Santa, Av Universitaria s/n, 02712, Nuevo Chimbote, Peru
| | - Lorenzo E Reyes-Flores
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences, Universidad Nacional del Santa, Av Universitaria s/n, 02712, Nuevo Chimbote, Peru
| | - Carmen Yzásiga-Barrera
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences, Universidad Nacional del Santa, Av Universitaria s/n, 02712, Nuevo Chimbote, Peru
| | - Eliana Zelada-Mázmela
- Laboratory of Genetics, Physiology, and Reproduction, Faculty of Sciences, Universidad Nacional del Santa, Av Universitaria s/n, 02712, Nuevo Chimbote, Peru.
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Dong MY, Lei L, Fan XW, Li YZ. Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes. AOB PLANTS 2021; 13:plab048. [PMID: 34567492 PMCID: PMC8459886 DOI: 10.1093/aobpla/plab048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Flowering in maize (Zea mays) is influenced by photoperiod. The CO, CO-like/COL and TOC1 (CCT) domain protein-encoding genes in maize, ZmCCTs, are particularly important for photoperiod sensitivity. However, little is known about CCT protein-encoding gene number across plant species or among maize inbred lines. Therefore, we analysed CCT protein-encoding gene number across plant species, and characterized ZmCCTs in different inbred lines, including structural variations (SVs), copy number variations (CNVs), expression under stresses, dark-dark (DD) and dark-light (DL) cycles, interaction network and associations with maize quantitative trait loci (QTLs) by referring to the latest v4 genome data of B73. Gene number varied greatly across plant species, more in polyploids than in diploids. The numbers of ZmCCTs identified were 58 in B73, 59 in W22, 48 in Mo17, and 57 in Huangzao4 for temperate maize inbred lines, and 68 in tropical maize inbred line SK. Some ZmCCTs underwent duplications and presented chromosome collinearity. Structural variations and CNVs were found but they had no germplasm specificity. Forty-two ZmCCTs responded to stresses. Expression of 37 ZmCCTs in embryonic leaves during seed germination of maize under DD and DL cycles was roughly divided into five patterns of uphill pattern, downhill-pattern, zigzag-pattern, └-pattern and ⅃-pattern, indicating some of them have a potential to perceive dark and/or dark-light transition. Thirty-three ZmCCTs were co-expressed with 218 other maize genes; and 24 ZmCCTs were associated with known QTLs. The data presented in this study will help inform further functions of ZmCCTs.
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Affiliation(s)
- Ming-You Dong
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - Ling Lei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - Xian-Wei Fan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
| | - You-Zhi Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi 530004, P. R. China
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Exploring Genetic Variability among and within Hail Tomato Landraces Based on Sequence-Related Amplified Polymorphism Markers. DIVERSITY 2021. [DOI: 10.3390/d13030135] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Landraces are valuable sources of genetic characteristics, which are of plant breeders’ interest to include in breeding programs for crop improvement. We assess the inter- and intra-genetic variability among 96 accessions representing three Hail tomato landrace using DNA-based marker sequence-related amplified polymorphism (SRAP). Seven SRAP primer combinations generated 55 alleles with a polymorphism of 100%, and an average of 7.86 polymorphic alleles per pair of primers. All primers showed an average of 0.68 polymorphic information content (PIC) value and discrimination power (DP) of 14.29. Principal coordinate analysis (PCoA) confirmed the clustering produced via the UPGMA similarity dendrogram allowed for the grouping of the 96 accessions according to its gene bank accession numbers and showed relatively good separation between landraces. A similarity value ranged from 0.04 to 1.0 among accessions of Hail 747, 0.05 to 1.0 in Hail 1072, and from 0.16 to 0.92 in Hail 548. These results showed the landraces harbor a wide range of genetic diversity at both inter and intra-variation levels. AMOVA showed that most of the genetic variation was because of differences within populations (87%). Tomato Hail landraces have well-differentiated genetic populations and admixtures, where Hail 747 formed their separate group, and both Hail 548 and Hail 1072 were admixed, and some accessions showed more diversity pattern. We have to take the SRAP technique’s effectiveness in the study of genetic variability among and within landraces into consideration in the tomato-breeding programs through marker-assessed selection.
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Wang D, Shen B, Gong H. Genetic diversity of Simao pine in China revealed by SRAP markers. PeerJ 2019; 7:e6529. [PMID: 30828500 PMCID: PMC6396742 DOI: 10.7717/peerj.6529] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 01/28/2019] [Indexed: 11/20/2022] Open
Abstract
Background Simao pine (Pinus kesiya Royle ex Gordon var. langbianensis (A. Chev.) Gaussen) is one of the most important tree species in the production of timber and resin in China. However, the genetic diversity of the natural populations has not been assessed to date. In this study, sequence related amplified polymorphism (SRAP) markers were used to investigate the genetic composition of natural Simao pine populations. Method The SRAP markers were applied and their efficiency was compared using various statistical multivariate methods, including analysis molecular of variance (AMOVA), the unweighted pair group method with arithmetic mean (UPGMA), and Principal coordinate analysis (PCoA). Results The 11 populations revealed a high level of genetic diversity (PPB = 95.45%, H = 0.4567, I = 0.6484) at the species level. A moderately low level of genetic differentiation (Gst = 0.1701), and a slightly high level of gene flow (Nm = 2.4403) were observed among populations using AMOVA. Eleven populations of Simao pine were gathered into four distinct clusters based on molecular data, and the results of UPGMA and PCoA also illustrated that assignment of populations is not completely consistent with geographic origin. The Mantel test revealed there was no significant correlation between geographic and genetic distance (r = 0.241, p = 0.090). Discussion The SRAP markers were very effective in the assessment of genetic diversity in Simao pine. Simao pine populations display high levels of genetic diversity and low or moderate levels of genetic differentiation due to frequent gene exchange among populations. The low genetic differentiation among populations implied that conservation efforts should aim to preserve all remaining natural populations of this species. The information derived from this study is useful when identifying populations and categorizing their population origins, making possible the design of long term management program such as genetic improvement by selective breeding.
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Affiliation(s)
- Dawei Wang
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China.,Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
| | - Bingqi Shen
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, Yunnan, China.,Key Laboratory for Forest Genetic and Tree Improvement & Propagation in Universities of Yunnan Province, Southwest Forestry University, Kunming, Yunnan, China
| | - Hede Gong
- School of Geography, Southwest Forestry University, Kunming, Yunnan, China
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