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Silveira DC, Weiler RL, Brunes AP, Simioni C, Mills A, Longhi J, Corrêa MVS, Nauderer C, Valentini A, Santos WMD, Dall'agnol M. REML/BLUP methodology for selection intraspecific hybrids of Paspalum notatum Flügge by multivariate analysis. AN ACAD BRAS CIENC 2024; 95:e20230137. [PMID: 38198400 DOI: 10.1590/0001-3765202320230137] [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: 02/08/2023] [Accepted: 07/25/2023] [Indexed: 01/12/2024] Open
Abstract
The Paspalum genus has potential for further genetic improvement because of its adaptability to different ecosystems and production of high yields for grazing livestock. We estimate the genetic parameters of 195 intraspecific P. notatum hybrids using Restricted Maximum Likelihood (REML), followed by selection based on Best Linear Unbiased Prediction (BLUP) through multivariate analysis. The intraspecific hybrids studied showed considerable genetic variability in the evaluated forage traits, displaying their potential for progression in subsequent stages of the genetic improvement program. Notably, plant height emerged as an important trait for indirect selection to enhance forage production. The use of the REML/BLUP procedure proves to be a robust tool for data analysis, particularly for perennial species. Furthermore, multivariate analysis based on BLUPs should be used in the selection process within breeding programs. Based on the BLUP values, hybrids D3, D16, C17, C2 and B17 were identified as superior for forage production, and they hold promise for future breeding programs for future breeding initiatives aimed at direct selection to improve yield.
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Affiliation(s)
- Diógenes C Silveira
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
| | - Roberto Luis Weiler
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
| | - André P Brunes
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
| | - Carine Simioni
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
| | - Annamaria Mills
- Field Research Centre, Lincoln University, Lincoln 7647, New Zealand
| | - Júlia Longhi
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
| | - Marcos Vinicius S Corrêa
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
| | - Carla Nauderer
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
| | - Arthur Valentini
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
| | - Weliton M Dos Santos
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
| | - Miguel Dall'agnol
- Universidade Federal do Rio Grande do Sul, Faculdade de Agronomia, Departamento de Plantas Forrageiras e Agrometeorologia, Av. Bento Gonçalves, 7712, 91501-970 Porto Alegre, RS, Brazil
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Munoz Santa I, Nagel S, Taylor JD. Incorporating the pedigree information in multi-environment trial analyses for improving common vetch. FRONTIERS IN PLANT SCIENCE 2023; 14:1166133. [PMID: 37655219 PMCID: PMC10467272 DOI: 10.3389/fpls.2023.1166133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 07/31/2023] [Indexed: 09/02/2023]
Abstract
Common vetch is one of the most profitable forage legumes due to its versatility in end-use which includes grain, hay, green manure, and silage. Furthermore, common vetch is one of the best crops to rotate with cereals as it can increase soil fertility which results in higher yield in cereal crops. The National Vetch Breeding Program located in South Australia is focused on developing new vetch varieties with higher grain and dry matter yields, better resistance to major diseases, and wider adaptability to Australian cropping environments. As part of this program, a study was conducted with 35 field trials from 2015 to 2021 in South Australia, Western Australia, Victoria, and New South Wales with the objective of determining the best parents for future crosses and the vetch lines with highest commercial value in terms of grain yield production. A total of 392 varieties were evaluated. The individual field trials were combined in a multi-environment trial data, where each trial is identified as an environment. Multiplicative mixed models were used to analyze the data and a factor analytic approach to model the genetic by environment interaction effects. The pedigree of the lines was then assembled and incorporated into the analysis. This approach allowed to partition the total effects into additive and non-additive components. The total and additive genetic effects were inspected across and within environments for broad and specific selections of the lines with the best commercial value and the best parents. Summary measures of overall performance and stability were used to aid with selection of parents. To the best of our knowledge, this is the first study which used the pedigree information to breed common vetch. In this paper, the application of this statistical methodology has been successfully implemented with the inclusion of the pedigree improving the fit of the models to the data with most of the total genetic variation explained by the additive heritable component. The results of this study have shown the importance of including the pedigree information for common vetch breeding programs and have improved the ability of breeders to select superior commercial lines and parents.
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Affiliation(s)
- Isabel Munoz Santa
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
- Department of Statistics and Operations Research, University of Valencia, Valencia, Spain
| | - Stuart Nagel
- South Australian Research and Development Institute, Adelaide, SA, Australia
| | - Julian Daniel Taylor
- School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, SA, Australia
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Agre PA, Edemodu A, Obidiegwu JE, Adebola P, Asiedu R, Asfaw A. Variability and genetic merits of white Guinea yam landraces in Nigeria. FRONTIERS IN PLANT SCIENCE 2023; 14:1051840. [PMID: 36814760 PMCID: PMC9940711 DOI: 10.3389/fpls.2023.1051840] [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: 09/23/2022] [Accepted: 01/09/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Landraces represent a significant gene pool of African cultivated white Guinea yam diversity. They could, therefore, serve as a potential donor of important traits such as resilience to stresses as well as food quality attributes that may be useful in modern yam breeding. This study assessed the pattern of genetic variability, quantitative trait loci (QTLs), alleles, and genetic merits of landraces, which could be exploited in breeding for more sustainable yam production in Africa. METHODS A total of 86 white Guinea yam landraces representing the popular landraces in Nigeria alongside 16 elite clones were used for this study. The yam landraces were genotyped using 4,819 DArTseq SNP markers and profiled using key productivity and food quality traits. RESULTS AND DISCUSSION Genetic population structure through admixture and hierarchical clustering methods revealed the presence of three major genetic groups. Genome-wide association scan identified thirteen SNP markers associated with five key traits, suggesting that landraces constitute a source of valuable genes for productivity and food quality traits. Further dissection of their genetic merits in yam breeding using the Genomic Prediction of Cross Performance (GPCP) allowed identifying several landraces with high crossing merit for multiple traits. Thirteen landraces were identified as potential genitors to develop segregating progenies to improve multiple traits simultaneously for desired gains in yam breeding. Results of this study provide valuable insights into the patterns and the merits of local genetic diversity which can be utilized for identifying desirable genes and alleles of interest in yam breeding for Africa.
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Affiliation(s)
- Paterne A. Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Alex Edemodu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Jude E. Obidiegwu
- National Root Crops Research Institute, Umudike, Abia State, Nigeria
| | - Patrick Adebola
- International Institute of Tropical Agriculture (IITA), Abuja, Nigeria
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Abuja, Nigeria
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Norman PE, Agre PA, Asiedu R, Asfaw A. Multiple-Traits Selection in White Guinea Yam ( Dioscorea rotundata) Genotypes. PLANTS (BASEL, SWITZERLAND) 2022; 11:3003. [PMID: 36365454 PMCID: PMC9658037 DOI: 10.3390/plants11213003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/04/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
Choosing superior parents with complementary trait values for hybridization and selecting variants with desired product profiles to release as a new cultivar are important breeding activities to progress genetic improvement in crops. This study assessed the genetic potential of 36 parental lines of white Guinea yam (Dioscorea rotundata) genotypes using multi-trait index-based factor analysis and ideotype design (FAI-BLUP). The experiment utilized 36 white yam genotypes laid out in a 6 × 6 triple lattice design with three replications and phenotyped for 18 agronomic and food quality traits. Findings showed significant differences among genotypes for all assessed traits. Fifteen traits had desired genetic gains, whereas stem diameter (-1.34%), and two starch property traits ((holding strength (-26.31%) and final paste viscosity (-3.33%)) had undesired selection gain. The FAI-BLUP index provided total genetic gains of 148.91% for traits desired for increase and -29.26% for those desired for decrease. Genotypes TDr08-21-2, TDr9518544, TDr9501932, TDr8902665 and Pampars were identified as top best candidate for simultaneous improvement of the measured traits in white yam breeding. The findings indicate the effectiveness of the FAI-BLUP index in identifying and selecting genotypes.
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Affiliation(s)
- Prince Emmanuel Norman
- Sierra Leone Agricultural Research Institute, Tower Hill, Freetown PMB 1313, Sierra Leone
- International Institute of Tropical Agriculture, Ibadan PMB 5320, Nigeria
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, Legon, Accra P.O. Box LG 30, Ghana
| | - Paterne A. Agre
- International Institute of Tropical Agriculture, Ibadan PMB 5320, Nigeria
| | - Robert Asiedu
- International Institute of Tropical Agriculture, Ibadan PMB 5320, Nigeria
| | - Asrat Asfaw
- International Institute of Tropical Agriculture, Ibadan PMB 5320, Nigeria
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Pirnajmedin F, Majidi MM, Taleb MH, Rostami D. Genetic parameters and selection in full-sib families of tall fescue using best linear unbiased prediction (BLUP) analysis. BMC PLANT BIOLOGY 2022; 22:293. [PMID: 35701757 PMCID: PMC9199132 DOI: 10.1186/s12870-022-03675-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Better understanding of genetic structure of economic traits is crucial for identification and selection of superior genotypes in specific breeding programs. Best linear unbiased prediction (BLUP) is the most efficient method in this regard, which is poorly used in forage plant breeding. The present study aimed to assess genetic variation, estimate genetic parameters, and predict breeding values of five essential traits in full sib families (recognized by EST-SSR markers) of tall fescue using REML/BLUP procedure. METHOD Forty-two full-sib families of tall fescue (included of 120 individual genotypes), recognized by EST-SSR markers along with twenty-one their corresponding parental genotypes were assessed for biomass production and agro-morphological traits at three harvests (spring, summer, and autumn) in the field during 4 years (2017-2020). RESULTS Considerable genotypic variability was observed for all traits. Low narrow-sense heritability (h2n) for dry forage yield (DFY) at three harvest indicates that non-additive gene actions may play an important role in the inheritance of this trait. Higher h2n of yield related traits and flowering time and also significant genetic correlation of these traits with forage yield, suggests that selection based on these traits may lead to indirect genetic improvement of DFY. CONCLUSION Our results showed the adequacy of REML/BLUP procedure for identification and selection of preferable parental genotypes and progenies with higher breeding values for future breeding programs such as variety development in tall fescue. Parental genotypes 21 M, 1 M, and 20 L were identified as superior and stable genotypes and could also produce the best hybrid combinations when they were mostly used as maternal parent.
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Affiliation(s)
- Fatemeh Pirnajmedin
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111 Iran
| | - Mohammad Mahdi Majidi
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111 Iran
| | - Mohammad Hadi Taleb
- Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111 Iran
| | - Davoud Rostami
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-83111 Iran
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Iseki K, Matsumoto R, Olaleye O, Shimizu M, Asfaw A. Variability of Flowering Sex and Its Effect on Agronomic Trait Expression in White Guinea Yam. FRONTIERS IN PLANT SCIENCE 2022; 13:837951. [PMID: 35548274 PMCID: PMC9083005 DOI: 10.3389/fpls.2022.837951] [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: 12/17/2021] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
White Guinea yam (Dioscorea rotundata) is mainly a dioecious tuberous crop that produces flowers of varying sex phenotypes. Agronomic traits in Guinea yam differ according to the sex phenotype, but the precise interaction between the traits and sex phenotype is not clearly understood. This might be due to the high heterozygosity of yam where cultivars with different flowering sex have different genetic backgrounds, which mask the sole effect of sex phenotype on the agronomic traits. This study used F1-derived clonal progenies from a bi-parental cross to minimize the impact of different genetic backgrounds among the plants with different sex phenotypes. The impact of plant sex on agronomic traits, specifically tuber yield, was evaluated through field trials conducted for four years. The results showed that only plants with a female genotype exhibited varying sex phenotypes even within the clones of same accession grown in the same experimental field. The significant effects of sex genotype and phenotype on agronomic traits were detected. Our results revealed that the flowering date was delayed in the plants with female genotypes compared to male genotypes, even when compared only among the plants with male phenotypes. The flowering date is the most important reason for the sexual differences in tuber yield. A high tuber yield was obtained when plants with the female phenotype flowered before tuber enlargement. This result can be attributed to the fact that the low flowering intensity in female plants increases the availability of carbon resources for leaf development. Female plants also showed a large negative effect of late flowering on tuber yield owing to resource competition between flowering and tuber enlargement. These findings demonstrate the feasibility of yield improvement by controlling the flowering time, with a higher effectiveness achieved in female than in male plants.
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Affiliation(s)
- Kohtaro Iseki
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Ryo Matsumoto
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Olajumoke Olaleye
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Motoki Shimizu
- Iwate Biotechnology Research Center (IBRC), Kitakami, Japan
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Diversity of Water Yam (Dioscorea alata L.) Accessions from Côte d’Ivoire Based on SNP Markers and Agronomic Traits. PLANTS 2021; 10:plants10122562. [PMID: 34961033 PMCID: PMC8705775 DOI: 10.3390/plants10122562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/16/2021] [Accepted: 11/19/2021] [Indexed: 11/24/2022]
Abstract
Dioscorea alata (L.), also referred to as water, winged, or greater yam, is one of the most economically important staple food crops in tropical and subtropical areas. In Côte d’Ivoire, it represents, along with other yam species, the largest food crop and significantly contributes to food security. However, studies focusing on better understanding the structure and extent of genetic diversity among D. alata accessions, using molecular and phenotypic traits, are limited. This study was, therefore, conducted to assess the pattern of genetic variability in a set of 188 D. alata accessions from the National Agronomic Research Centre (CNRA) genebank using 11,722 SNP markers (generated by the Diversity Arrays Technology) and nine agronomic traits. Phylogenetic analyses using hierarchical clustering, admixture, kinship, and Discriminant analysis of principal component (DAPC) all assigned the accessions into four main clusters. Genetic diversity assessment using molecular-based SNP markers showed a high proportion of polymorphic SNPs (87.81%). The analysis of molecular variance (AMOVA) showed low molecular variability within genetic groups. In addition, the agronomic traits evaluated for two years in field conditions showed a high heritability and high variability among D. alata accessions. This study provides insights into the genetic diversity among accessions in the CNRA genebank and opens an avenue for sustainable resource management and the identification of promising parental clones for water yam breeding programs in Côte d’Ivoire.
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