STABILITYSOFT: A new online program to calculate parametric and non‐parametric stability statistics for crop traits
Premise of the Study Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype‐by‐environment interactions (GEI) occur for quantitative traits such as reproductive fitne...
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| Published in | Applications in plant sciences Vol. 7; no. 1; pp. e01211 - n/a |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
John Wiley & Sons, Inc
01.01.2019
John Wiley and Sons Inc |
| Subjects | |
| Online Access | Get full text |
| ISSN | 2168-0450 2168-0450 |
| DOI | 10.1002/aps3.1211 |
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| Abstract | Premise of the Study
Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype‐by‐environment interactions (GEI) occur for quantitative traits such as reproductive fitness, longevity, height, weight, yield, and disease resistance. The stability of genotypes across a range of environments can be analyzed using GEI analysis. GEI analysis includes univariate and multivariate analyses with both parametric and non‐parametric models.
Methods and Results
The program STABILITYSOFT is online software based on JavaScript and R to calculate several univariate parametric and non‐parametric statistics for various crop traits. These statistics include Plaisted and Peterson's mean variance component (θi), Plaisted's GE variance component (θ(i)), Wricke's ecovalence stability index (Wi2), regression coefficient (bi), deviation from regression (Sdi2), Shukla's stability variance (σi2), environmental coefficient of variance (CVi), Nassar and Huhn's statistics (S(1), S(2)), Huhn's equation (S(3) and S(6)), Thennarasu's non‐parametric statistics (NP(i)), and Kang's rank‐sum. These statistics are important in the identification of stable genotypes; hence, this program can compare and select genotypes across multiple environment trials for a given data set. This program supports both the repeated data across environments and matrix data types. The accuracy of the results obtained from this software was tested on several crop plants.
Conclusions
This new software provides a user‐friendly interface to estimate stability statistics accurately for plant scientists, agronomists, and breeders who deal with large volumes of quantitative data. This software can also show ranking patterns of genotypes and describe associations among different statistics with yield performance through a heat map plot. The software is available at https://mohsenyousefian.com/stabilitysoft/. |
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| AbstractList | PREMISE OF THE STUDY: Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype‐by‐environment interactions (GEI) occur for quantitative traits such as reproductive fitness, longevity, height, weight, yield, and disease resistance. The stability of genotypes across a range of environments can be analyzed using GEI analysis. GEI analysis includes univariate and multivariate analyses with both parametric and non‐parametric models. METHODS AND RESULTS: The program STABILITYSOFT is online software based on JavaScript and R to calculate several univariate parametric and non‐parametric statistics for various crop traits. These statistics include Plaisted and Peterson's mean variance component (θᵢ), Plaisted's GE variance component (θ₍ᵢ₎), Wricke's ecovalence stability index (Wᵢ²), regression coefficient (bᵢ), deviation from regression (Sdᵢ²), Shukla's stability variance (σᵢ²), environmental coefficient of variance (CVᵢ), Nassar and Huhn's statistics (S⁽¹⁾, S⁽²⁾), Huhn's equation (S⁽³⁾ and S⁽⁶⁾), Thennarasu's non‐parametric statistics (NP⁽ⁱ⁾), and Kang's rank‐sum. These statistics are important in the identification of stable genotypes; hence, this program can compare and select genotypes across multiple environment trials for a given data set. This program supports both the repeated data across environments and matrix data types. The accuracy of the results obtained from this software was tested on several crop plants. CONCLUSIONS: This new software provides a user‐friendly interface to estimate stability statistics accurately for plant scientists, agronomists, and breeders who deal with large volumes of quantitative data. This software can also show ranking patterns of genotypes and describe associations among different statistics with yield performance through a heat map plot. The software is available at https://mohsenyousefian.com/stabilitysoft/. Premise of the Study Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype‐by‐environment interactions (GEI) occur for quantitative traits such as reproductive fitness, longevity, height, weight, yield, and disease resistance. The stability of genotypes across a range of environments can be analyzed using GEI analysis. GEI analysis includes univariate and multivariate analyses with both parametric and non‐parametric models. Methods and Results The program STABILITYSOFT is online software based on JavaScript and R to calculate several univariate parametric and non‐parametric statistics for various crop traits. These statistics include Plaisted and Peterson's mean variance component (θi), Plaisted's GE variance component (θ(i)), Wricke's ecovalence stability index (Wi2), regression coefficient (bi), deviation from regression (Sdi2), Shukla's stability variance (σi2), environmental coefficient of variance (CVi), Nassar and Huhn's statistics (S(1), S(2)), Huhn's equation (S(3) and S(6)), Thennarasu's non‐parametric statistics (NP(i)), and Kang's rank‐sum. These statistics are important in the identification of stable genotypes; hence, this program can compare and select genotypes across multiple environment trials for a given data set. This program supports both the repeated data across environments and matrix data types. The accuracy of the results obtained from this software was tested on several crop plants. Conclusions This new software provides a user‐friendly interface to estimate stability statistics accurately for plant scientists, agronomists, and breeders who deal with large volumes of quantitative data. This software can also show ranking patterns of genotypes and describe associations among different statistics with yield performance through a heat map plot. The software is available at https://mohsenyousefian.com/stabilitysoft/. Premise of the StudyAccess to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype‐by‐environment interactions (GEI) occur for quantitative traits such as reproductive fitness, longevity, height, weight, yield, and disease resistance. The stability of genotypes across a range of environments can be analyzed using GEI analysis. GEI analysis includes univariate and multivariate analyses with both parametric and non‐parametric models.Methods and ResultsThe program STABILITYSOFT is online software based on JavaScript and R to calculate several univariate parametric and non‐parametric statistics for various crop traits. These statistics include Plaisted and Peterson's mean variance component (θi), Plaisted's GE variance component (θ(i)), Wricke's ecovalence stability index (Wi2), regression coefficient (bi), deviation from regression (Sdi2), Shukla's stability variance (σi2), environmental coefficient of variance (CVi), Nassar and Huhn's statistics (S(1), S(2)), Huhn's equation (S(3) and S(6)), Thennarasu's non‐parametric statistics (NP(i)), and Kang's rank‐sum. These statistics are important in the identification of stable genotypes; hence, this program can compare and select genotypes across multiple environment trials for a given data set. This program supports both the repeated data across environments and matrix data types. The accuracy of the results obtained from this software was tested on several crop plants.ConclusionsThis new software provides a user‐friendly interface to estimate stability statistics accurately for plant scientists, agronomists, and breeders who deal with large volumes of quantitative data. This software can also show ranking patterns of genotypes and describe associations among different statistics with yield performance through a heat map plot. The software is available at https://mohsenyousefian.com/stabilitysoft/. Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype-by-environment interactions (GEI) occur for quantitative traits such as reproductive fitness, longevity, height, weight, yield, and disease resistance. The stability of genotypes across a range of environments can be analyzed using GEI analysis. GEI analysis includes univariate and multivariate analyses with both parametric and non-parametric models. The program STABILITYSOFT is online software based on JavaScript and R to calculate several univariate parametric and non-parametric statistics for various crop traits. These statistics include Plaisted and Peterson's mean variance component ( ), Plaisted's GE variance component ( ), Wricke's ecovalence stability index ( ), regression coefficient ( ), deviation from regression ( ), Shukla's stability variance ( ), environmental coefficient of variance ( ), Nassar and Huhn's statistics ( , ), Huhn's equation ( and ), Thennarasu's non-parametric statistics ( ), and Kang's rank-sum. These statistics are important in the identification of stable genotypes; hence, this program can compare and select genotypes across multiple environment trials for a given data set. This program supports both the repeated data across environments and matrix data types. The accuracy of the results obtained from this software was tested on several crop plants. This new software provides a user-friendly interface to estimate stability statistics accurately for plant scientists, agronomists, and breeders who deal with large volumes of quantitative data. This software can also show ranking patterns of genotypes and describe associations among different statistics with yield performance through a heat map plot. The software is available at https://mohsenyousefian.com/stabilitysoft/. Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype-by-environment interactions (GEI) occur for quantitative traits such as reproductive fitness, longevity, height, weight, yield, and disease resistance. The stability of genotypes across a range of environments can be analyzed using GEI analysis. GEI analysis includes univariate and multivariate analyses with both parametric and non-parametric models.PREMISE OF THE STUDYAccess to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and qualitative traits. Genotype-by-environment interactions (GEI) occur for quantitative traits such as reproductive fitness, longevity, height, weight, yield, and disease resistance. The stability of genotypes across a range of environments can be analyzed using GEI analysis. GEI analysis includes univariate and multivariate analyses with both parametric and non-parametric models.The program STABILITYSOFT is online software based on JavaScript and R to calculate several univariate parametric and non-parametric statistics for various crop traits. These statistics include Plaisted and Peterson's mean variance component (θ i ), Plaisted's GE variance component (θ (i) ), Wricke's ecovalence stability index (W i 2 ), regression coefficient (b i ), deviation from regression (S di 2 ), Shukla's stability variance (σ i 2 ), environmental coefficient of variance (CV i ), Nassar and Huhn's statistics (S (1) , S (2) ), Huhn's equation (S (3) and S (6) ), Thennarasu's non-parametric statistics (NP (i) ), and Kang's rank-sum. These statistics are important in the identification of stable genotypes; hence, this program can compare and select genotypes across multiple environment trials for a given data set. This program supports both the repeated data across environments and matrix data types. The accuracy of the results obtained from this software was tested on several crop plants.METHODS AND RESULTSThe program STABILITYSOFT is online software based on JavaScript and R to calculate several univariate parametric and non-parametric statistics for various crop traits. These statistics include Plaisted and Peterson's mean variance component (θ i ), Plaisted's GE variance component (θ (i) ), Wricke's ecovalence stability index (W i 2 ), regression coefficient (b i ), deviation from regression (S di 2 ), Shukla's stability variance (σ i 2 ), environmental coefficient of variance (CV i ), Nassar and Huhn's statistics (S (1) , S (2) ), Huhn's equation (S (3) and S (6) ), Thennarasu's non-parametric statistics (NP (i) ), and Kang's rank-sum. These statistics are important in the identification of stable genotypes; hence, this program can compare and select genotypes across multiple environment trials for a given data set. This program supports both the repeated data across environments and matrix data types. The accuracy of the results obtained from this software was tested on several crop plants.This new software provides a user-friendly interface to estimate stability statistics accurately for plant scientists, agronomists, and breeders who deal with large volumes of quantitative data. This software can also show ranking patterns of genotypes and describe associations among different statistics with yield performance through a heat map plot. The software is available at https://mohsenyousefian.com/stabilitysoft/.CONCLUSIONSThis new software provides a user-friendly interface to estimate stability statistics accurately for plant scientists, agronomists, and breeders who deal with large volumes of quantitative data. This software can also show ranking patterns of genotypes and describe associations among different statistics with yield performance through a heat map plot. The software is available at https://mohsenyousefian.com/stabilitysoft/. |
| Author | Moradkhani, Hoda Yousefian, Mohsen Poczai, Peter Siddique, Kadambot H. M. Pour‐Aboughadareh, Alireza |
| AuthorAffiliation | 2 Dr. Hashtroudi Pre‐University Center Tehran Iran 5 The UWA Institute of Agriculture The University of Western Australia LB 5005 Perth Western Australia 6001 Australia 1 Department of Agronomy and Plant Breeding College of Agriculture and Natural Resources University of Tehran Karaj Iran 3 Department of Biotechnology and Plant Breeding Kermanshah Branch Islamic Azad University Kermanshah Iran 4 Botany Unit Finnish Museum of Natural History University of Helsinki P.O. Box 7 Helsinki FI‐00014 Finland |
| AuthorAffiliation_xml | – name: 3 Department of Biotechnology and Plant Breeding Kermanshah Branch Islamic Azad University Kermanshah Iran – name: 4 Botany Unit Finnish Museum of Natural History University of Helsinki P.O. Box 7 Helsinki FI‐00014 Finland – name: 2 Dr. Hashtroudi Pre‐University Center Tehran Iran – name: 1 Department of Agronomy and Plant Breeding College of Agriculture and Natural Resources University of Tehran Karaj Iran – name: 5 The UWA Institute of Agriculture The University of Western Australia LB 5005 Perth Western Australia 6001 Australia |
| Author_xml | – sequence: 1 givenname: Alireza orcidid: 0000-0001-5782-5327 surname: Pour‐Aboughadareh fullname: Pour‐Aboughadareh, Alireza organization: University of Tehran – sequence: 2 givenname: Mohsen orcidid: 0000-0002-5839-7317 surname: Yousefian fullname: Yousefian, Mohsen organization: Dr. Hashtroudi Pre‐University Center – sequence: 3 givenname: Hoda surname: Moradkhani fullname: Moradkhani, Hoda organization: Islamic Azad University – sequence: 4 givenname: Peter orcidid: 0000-0002-0107-1068 surname: Poczai fullname: Poczai, Peter email: peter.poczai@helsinki.fi organization: University of Helsinki – sequence: 5 givenname: Kadambot H. M. orcidid: 0000-0001-6097-4235 surname: Siddique fullname: Siddique, Kadambot H. M. organization: The University of Western Australia |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/30693157$$D View this record in MEDLINE/PubMed |
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| References | 1991; 19 2015; 17 1960; 37 2016; 108 1966; 6 1988; 16 2017; 45 1988; 101 2000; 92 1995 1978; 58 2016; 18 2012; 13 2016; 38 2018; 64 1972; 29 1963; 14 1987; 43 1990; 47 2002; 42 1895; 58 1962; 47 2018 2015 1959; 36 1999; 91 1998; 56 Crossa J. (e_1_2_6_6_1) 2012; 13 e_1_2_6_10_1 e_1_2_6_19_1 Khalili M. (e_1_2_6_18_1) 2016; 18 e_1_2_6_13_1 Wricke G. (e_1_2_6_28_1) 1962; 47 e_1_2_6_11_1 e_1_2_6_12_1 Akbarpour O. A. (e_1_2_6_3_1) 2016; 38 e_1_2_6_15_1 e_1_2_6_21_1 e_1_2_6_20_1 Ahmadi J. (e_1_2_6_2_1) 2015; 17 e_1_2_6_9_1 e_1_2_6_8_1 Kang M. S. (e_1_2_6_16_1) 1988; 16 Vaezi B. (e_1_2_6_26_1) 2017; 45 e_1_2_6_5_1 e_1_2_6_4_1 e_1_2_6_7_1 Huhn M. (e_1_2_6_14_1) 1990; 47 e_1_2_6_25_1 e_1_2_6_24_1 e_1_2_6_23_1 e_1_2_6_22_1 e_1_2_6_29_1 e_1_2_6_27_1 Kang M. S. (e_1_2_6_17_1) 1991; 19 |
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Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are... Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined by quantitative and... Premise of the StudyAccess to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are determined... PREMISE OF THE STUDY: Access to improved crop cultivars is the foundation for successful agriculture. New cultivars must have improved yields that are... |
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| SubjectTerms | adaptability Agricultural production Computer programs computer software Crops Cultivars data collection Disease resistance equations Genotype & phenotype genotype-environment interaction Genotype-environment interactions Genotypes heat Internet longevity Nonparametric statistics Operating systems phenotypic stability Plant breeding Plant sciences quantitative traits ranking method regression analysis Reproductive fitness Researchers Software Software Note Software Notes STABILITYSOFT Statistical analysis Statistics user interface variance |
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| Title | STABILITYSOFT: A new online program to calculate parametric and non‐parametric stability statistics for crop traits |
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