Tesi etd-04022020-125100
Link copiato negli appunti
Tipo di tesi
Dottorato
Autore
WOLDEYOHANNES, AEMIRO BEZABIH
URN
etd-04022020-125100
Titolo
Harnessing climatic, phenotypic, molecular and farmers priority traits in characterizing and valorizing teff genetic resources
Settore scientifico disciplinare
Istituto di Scienze della Vita
Corso di studi
SCIENZE AGRARIE E BIOTECNOLOGIE - AGROBIODIVERSITY
Commissione
relatore Prof. PE', MARIO ENRICO
Parole chiave
- Eragrostis
- teff
- yield
- agrobiodiversity
- breeding
- smallholder agriculture
- neglected and underultized crops
Data inizio appello
30/03/2021;
Disponibilità
completa
Riassunto analitico
Summary
Teff (Eragrostis tef (Zuccagni) Trotter) is an allotetraploid (AABB type genome; 2n = 4x = 40; ∼730 Mbp genome size) crop species belong to the grass family (Gramineae or Poaceae), subfamily Chlorodoidae, tribe Eragrostidae, sub-tribe Eragrosteae, and genus Eragrostis. The crop is one of the major cereal crop in terms of social and economic importance for millions of growers and consumers in Ethiopia. Among the major cereals cultivated in Ethiopia, teff stands first in the total area ( >3 million ha per year) and second to maize in the total grain production and the number of households involved in its production (Central Statistical Agency 2018). However, due to different biotic and abiotic production constraints, teff productivity remained very low (~ 1.76 tons per hectare) in teff farming system. In order to address these production challenges of teff as well as needs of smallholder farmers, it is advisable to conserve, characterize and valorize the locally adapted indigenous teff genetic resources. In addition, the Ethiopian teff research system needs to adopt the most advanced crop breeding approaches that integrate the latest advances in biosciences with traditional breeding programs and participatory approach. This thesis can be grouped into two major components, including review and characterization components.
The first component was reviewing literature on Eragrostis species genetic resource, their potential contribution and strategies to enhance teff productivity using various promising research approaches. This review paper emphasizes breeding significance of Eragrostis genetic resources and suggest recommendation about gaps related to accessions management at a national gene bank ; also, it highlights the challenges of teff farming in Ethiopia. Further, this review paper discuss about the exploration of Eragrostis genetic resources diversity for traits potential and trait based breeding, its valorization in appropriate breeding and farmer knowledge at maximizing the final grain yield and farmer prefered traits
The second component of the thesis was aimed at characterizing and valorizing the indigenous teff genetic resource collection through integrated climatic, phenotypic, molecular and indigenous knowledge of farmer-based evaluation of teff diversity to allow the proper management and efficient valorization of the Eragrostis gene pool for teff breeding and improvement program. This component was conducted in 4 main phases including a purification and future climate change prediction in Ethiopia (Chapter 3), panicle amplification for core selection, phenotyping with the participation of men and womenfarmers (Chapter 4) and genotyping for different purpose (Chapter 5).
The phenotypic and climatic characterization of large teff germplasm was the first phase of the study. A field experiment was conducted on 3850 teff accessions and the most frequent variant in each plot was considered the dominant phenotype for each accession, and was tagged and used for phenotyping. The result showed a wide range of diversity exists in teff collections both in terms of adaptation and agronomic traits (Chapter 3), which is connected with the climatic diversity existing across the teff growing area and to the socio-cultural process linked to its cultivation and trade. The study showed that teff accessions are cultivated in a broad range of environments with markedly diverse bioclimatic features and a broad variation was unveiled for a number of traits of breeding relevance. The combination of phenotypic and pedoclimatic diversity in the collection showed a differential distribution of trait values in relation to different adaptation niches, suggesting the potential of the EBI teff genetic resource for breeding. These observations advise future efforts aiming at selection and improvement of teff genetic resources to focus on different areas and altitude classes without meaningful bias. Future climate projections in Ethiopia showed that the suitability of teff cultivation will diminish by 2070 due to climate change, indicating the need for continuous breeding and conservation efforts. Thus, sustainable collection, conservation and valorization of Eragrostis genetic resource are vital for future breeding strategy in teff improvement program.
Selection of core collection from dominant phenotype in the large collection of teff accessions and amplification of panicles was the second phase of the study. We selected a core collection of teff landraces to represent the large active collection of teff germplasm at EBI. The method on selection of the core collection genotype was using five criteria: (1) Passport data of each teff accession including region of orgin and altitude catagories (2) Visible morphological variation such as seed and panicle color and panicle type and potential of secondary branching bearing the spikelet from the main axis (3) Grain yield potential as evaluated in quantitative and qualitative characterization of the collection (4) phenological traits (5) Lodging resistance. More than 10% of teff accessions were selected to constitute a core subset of 455 teff accessions including old and newly collected teff accessions. The amplification of the core collection of each representative panicle was carried out separately in a single row at the Koga irrigation site in 2018 off-season (December 2017 to May 2018) to obtain enough amount seed for field phenotyping.
The third phase of the study was conducting an integrated participatory evaluation of the core collection (Chapter 4). This activity aimed at identifying and analyzing farmer traits and to understand and determine the magnitude of variation and relationship for quantitative traits and indigenous knowledge of farmer traits in high potential teff growing areas of Ethiopia. The five hundred teff genotypes consisting of 455 core collections, 41 improved varieties and 4 breeding lines were phenotyped with the involvement of men and women farmers at two environments, Adet and Akaki under rain fed condition in the 2018 cropping season. High diversity of farmer traits exists in high potential teff growing areas of Ethiopia. Farmer traits are diverse and are related to their desire to meet economic, social and agro ecological conditions , which are reflected in our farmer trait selection of morphological, agronomic, and adaptive and market traits. Some traits had a marked difference in between environments and gender, showing the relative importance selection criteria of teff in specific environment and gender. Farmers have shown their own way of evaluating and selecting a genotype for their environments. In addition, the result showed that variation of useful traits among quantitative traits in the core collection. The high phenotypic traits diversity identified among the core collections can be used to develop new Eragrostis teff varieties. This study provides valuable information for future breeding projects targeting agronomic and farmer priority trait enhancement in teff.
Molecular diversity analysis in the Eragrostis species was the fourth phase of the study, which has great significance in enhancing improvement effort and for sustainable collection and valorization. Four hundred two genotypes consisting of 347 core collections, 37 improved varieties and 10 breeding lines and 7 wild relatives were selected for genotyped using SNP markers for the analysis of molecular variability and phenotype genotype association study. More than 10% of teff accessions were selected to constitute a core subset of 402 teff accessions.
GBS was performed on the 402 genotypes using Illumina HiSeq2000 machine. The number of genoyped loci and the number of polymorphic loci were 113,862 and 87,443, respectively. The number of filtered SNP or the overall genotyping effort resulted in 16870 SNP distributed genome-wise. The genetic distances among pairs of Eragrostis spp ranged from 0.0124 to 0.4254 with the mean value of 0.2946. This result could provide useful information for selecting distant parent to be used in cross breeding to get better traits combination for enhancing breeding effort. The highest mean genetic distance of genotypes was recorded for wild relatives. Thus, this species could be used as a source of unique gene in the improvement of teff breeding though hybridization and crosses can be made between the elite adapted teff cultivars with wild relatives to enrich genetic diversity in Eragrostis teff. A phylogenetic analysis identified VIII subgroup clades with variable sizes of 7 to 104 genotypes and it showed a higher admixture among teff landraces regardless of their collection origins and adaptation zone that could be due to the presence of continuous exchange of seeds among farmers throughout the country. The SNP dataset will be used for performing the GWAS to exploit the specific gene variation for economic traits in the phenotyped core collection of teff.
This thesis aimed at characterizing and valorizing the indigenous teff genetic resource collection through integrated climatic, phenotypic, molecular and indigenous knowledge of farmer-based evaluation of teff diversity to allow the proper management and efficient valorization of the Eragrostis gene pool for teff breeding and improvement program. The study was conducted in 4 main phases including a purification and future climate change prediction in Ethiopia (Chapter 2), panicle amplification for core selection, phenotyping with the participation of men and women farmers (Chapter 3) and genotyping for different purpose (Chapter 4). The following are the major findings of this thesis:
• A wide range of diversity exists in teff collections both in terms of adaptation and agronomic traits, which is connected with the climatic diversity existing across the teff growing area and to the socio-cultural process linked to its cultivation and trade. These observations advise future efforts aiming at selection and improvement of teff genetic resources to focus on different areas and altitude classes without meaningful bias;
• The study showed that teff accessions are cultivated in a broad range of environments with markedly diverse bioclimatic features and a broad variation was unveiled for a number of traits of breeding relevance;
• The combination of phenotypic and pedoclimatic diversity in the collection showed a differential distribution of trait values in relation to different adaptation niches. The agronomic traits of teff correlated with environmental variation at growing sites;
• Future climate projections in Ethiopia showed that the suitability of teff cultivation will diminish by 2070 due to climate change;
• High diversity of farmer traits exists in high potential teff growing areas of Ethiopia, which are significantly contributed by the diversity of landraces. Farmer traits are diverse and are related to their desire to meet economic, social and agro ecological conditions, which are reflected in our farmer trait selection of morphological, agronomic, and adaptive and market traits;
• Some traits had a marked difference in between environments and gender, showing the relative importance selection criteria of teff in specific environment and gender. Farmers have shown their own way of evaluating and selecting a genotype for their environments;
• Teff molecular diversity is elevated. A phylogenetic analysis identified VIII subgroup clades with variable sizes of 7 to 104 genotypes. The results could provide useful information for selecting distant parent to be used in cross breeding to get better traits combination for enhancing breeding effort. The SNP dataset will be used for performing the GWAS to exploit the specific gene variation for economic traits in the phenotyped core collection of teff.
Keywords Ethiopia; smallholder agriculture; bioclim; species distribution modelling; Eragrostis tef; phenotypes, farmer traits, SNP, diversity
Teff (Eragrostis tef (Zuccagni) Trotter) is an allotetraploid (AABB type genome; 2n = 4x = 40; ∼730 Mbp genome size) crop species belong to the grass family (Gramineae or Poaceae), subfamily Chlorodoidae, tribe Eragrostidae, sub-tribe Eragrosteae, and genus Eragrostis. The crop is one of the major cereal crop in terms of social and economic importance for millions of growers and consumers in Ethiopia. Among the major cereals cultivated in Ethiopia, teff stands first in the total area ( >3 million ha per year) and second to maize in the total grain production and the number of households involved in its production (Central Statistical Agency 2018). However, due to different biotic and abiotic production constraints, teff productivity remained very low (~ 1.76 tons per hectare) in teff farming system. In order to address these production challenges of teff as well as needs of smallholder farmers, it is advisable to conserve, characterize and valorize the locally adapted indigenous teff genetic resources. In addition, the Ethiopian teff research system needs to adopt the most advanced crop breeding approaches that integrate the latest advances in biosciences with traditional breeding programs and participatory approach. This thesis can be grouped into two major components, including review and characterization components.
The first component was reviewing literature on Eragrostis species genetic resource, their potential contribution and strategies to enhance teff productivity using various promising research approaches. This review paper emphasizes breeding significance of Eragrostis genetic resources and suggest recommendation about gaps related to accessions management at a national gene bank ; also, it highlights the challenges of teff farming in Ethiopia. Further, this review paper discuss about the exploration of Eragrostis genetic resources diversity for traits potential and trait based breeding, its valorization in appropriate breeding and farmer knowledge at maximizing the final grain yield and farmer prefered traits
The second component of the thesis was aimed at characterizing and valorizing the indigenous teff genetic resource collection through integrated climatic, phenotypic, molecular and indigenous knowledge of farmer-based evaluation of teff diversity to allow the proper management and efficient valorization of the Eragrostis gene pool for teff breeding and improvement program. This component was conducted in 4 main phases including a purification and future climate change prediction in Ethiopia (Chapter 3), panicle amplification for core selection, phenotyping with the participation of men and womenfarmers (Chapter 4) and genotyping for different purpose (Chapter 5).
The phenotypic and climatic characterization of large teff germplasm was the first phase of the study. A field experiment was conducted on 3850 teff accessions and the most frequent variant in each plot was considered the dominant phenotype for each accession, and was tagged and used for phenotyping. The result showed a wide range of diversity exists in teff collections both in terms of adaptation and agronomic traits (Chapter 3), which is connected with the climatic diversity existing across the teff growing area and to the socio-cultural process linked to its cultivation and trade. The study showed that teff accessions are cultivated in a broad range of environments with markedly diverse bioclimatic features and a broad variation was unveiled for a number of traits of breeding relevance. The combination of phenotypic and pedoclimatic diversity in the collection showed a differential distribution of trait values in relation to different adaptation niches, suggesting the potential of the EBI teff genetic resource for breeding. These observations advise future efforts aiming at selection and improvement of teff genetic resources to focus on different areas and altitude classes without meaningful bias. Future climate projections in Ethiopia showed that the suitability of teff cultivation will diminish by 2070 due to climate change, indicating the need for continuous breeding and conservation efforts. Thus, sustainable collection, conservation and valorization of Eragrostis genetic resource are vital for future breeding strategy in teff improvement program.
Selection of core collection from dominant phenotype in the large collection of teff accessions and amplification of panicles was the second phase of the study. We selected a core collection of teff landraces to represent the large active collection of teff germplasm at EBI. The method on selection of the core collection genotype was using five criteria: (1) Passport data of each teff accession including region of orgin and altitude catagories (2) Visible morphological variation such as seed and panicle color and panicle type and potential of secondary branching bearing the spikelet from the main axis (3) Grain yield potential as evaluated in quantitative and qualitative characterization of the collection (4) phenological traits (5) Lodging resistance. More than 10% of teff accessions were selected to constitute a core subset of 455 teff accessions including old and newly collected teff accessions. The amplification of the core collection of each representative panicle was carried out separately in a single row at the Koga irrigation site in 2018 off-season (December 2017 to May 2018) to obtain enough amount seed for field phenotyping.
The third phase of the study was conducting an integrated participatory evaluation of the core collection (Chapter 4). This activity aimed at identifying and analyzing farmer traits and to understand and determine the magnitude of variation and relationship for quantitative traits and indigenous knowledge of farmer traits in high potential teff growing areas of Ethiopia. The five hundred teff genotypes consisting of 455 core collections, 41 improved varieties and 4 breeding lines were phenotyped with the involvement of men and women farmers at two environments, Adet and Akaki under rain fed condition in the 2018 cropping season. High diversity of farmer traits exists in high potential teff growing areas of Ethiopia. Farmer traits are diverse and are related to their desire to meet economic, social and agro ecological conditions , which are reflected in our farmer trait selection of morphological, agronomic, and adaptive and market traits. Some traits had a marked difference in between environments and gender, showing the relative importance selection criteria of teff in specific environment and gender. Farmers have shown their own way of evaluating and selecting a genotype for their environments. In addition, the result showed that variation of useful traits among quantitative traits in the core collection. The high phenotypic traits diversity identified among the core collections can be used to develop new Eragrostis teff varieties. This study provides valuable information for future breeding projects targeting agronomic and farmer priority trait enhancement in teff.
Molecular diversity analysis in the Eragrostis species was the fourth phase of the study, which has great significance in enhancing improvement effort and for sustainable collection and valorization. Four hundred two genotypes consisting of 347 core collections, 37 improved varieties and 10 breeding lines and 7 wild relatives were selected for genotyped using SNP markers for the analysis of molecular variability and phenotype genotype association study. More than 10% of teff accessions were selected to constitute a core subset of 402 teff accessions.
GBS was performed on the 402 genotypes using Illumina HiSeq2000 machine. The number of genoyped loci and the number of polymorphic loci were 113,862 and 87,443, respectively. The number of filtered SNP or the overall genotyping effort resulted in 16870 SNP distributed genome-wise. The genetic distances among pairs of Eragrostis spp ranged from 0.0124 to 0.4254 with the mean value of 0.2946. This result could provide useful information for selecting distant parent to be used in cross breeding to get better traits combination for enhancing breeding effort. The highest mean genetic distance of genotypes was recorded for wild relatives. Thus, this species could be used as a source of unique gene in the improvement of teff breeding though hybridization and crosses can be made between the elite adapted teff cultivars with wild relatives to enrich genetic diversity in Eragrostis teff. A phylogenetic analysis identified VIII subgroup clades with variable sizes of 7 to 104 genotypes and it showed a higher admixture among teff landraces regardless of their collection origins and adaptation zone that could be due to the presence of continuous exchange of seeds among farmers throughout the country. The SNP dataset will be used for performing the GWAS to exploit the specific gene variation for economic traits in the phenotyped core collection of teff.
This thesis aimed at characterizing and valorizing the indigenous teff genetic resource collection through integrated climatic, phenotypic, molecular and indigenous knowledge of farmer-based evaluation of teff diversity to allow the proper management and efficient valorization of the Eragrostis gene pool for teff breeding and improvement program. The study was conducted in 4 main phases including a purification and future climate change prediction in Ethiopia (Chapter 2), panicle amplification for core selection, phenotyping with the participation of men and women farmers (Chapter 3) and genotyping for different purpose (Chapter 4). The following are the major findings of this thesis:
• A wide range of diversity exists in teff collections both in terms of adaptation and agronomic traits, which is connected with the climatic diversity existing across the teff growing area and to the socio-cultural process linked to its cultivation and trade. These observations advise future efforts aiming at selection and improvement of teff genetic resources to focus on different areas and altitude classes without meaningful bias;
• The study showed that teff accessions are cultivated in a broad range of environments with markedly diverse bioclimatic features and a broad variation was unveiled for a number of traits of breeding relevance;
• The combination of phenotypic and pedoclimatic diversity in the collection showed a differential distribution of trait values in relation to different adaptation niches. The agronomic traits of teff correlated with environmental variation at growing sites;
• Future climate projections in Ethiopia showed that the suitability of teff cultivation will diminish by 2070 due to climate change;
• High diversity of farmer traits exists in high potential teff growing areas of Ethiopia, which are significantly contributed by the diversity of landraces. Farmer traits are diverse and are related to their desire to meet economic, social and agro ecological conditions, which are reflected in our farmer trait selection of morphological, agronomic, and adaptive and market traits;
• Some traits had a marked difference in between environments and gender, showing the relative importance selection criteria of teff in specific environment and gender. Farmers have shown their own way of evaluating and selecting a genotype for their environments;
• Teff molecular diversity is elevated. A phylogenetic analysis identified VIII subgroup clades with variable sizes of 7 to 104 genotypes. The results could provide useful information for selecting distant parent to be used in cross breeding to get better traits combination for enhancing breeding effort. The SNP dataset will be used for performing the GWAS to exploit the specific gene variation for economic traits in the phenotyped core collection of teff.
Keywords Ethiopia; smallholder agriculture; bioclim; species distribution modelling; Eragrostis tef; phenotypes, farmer traits, SNP, diversity
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