Special Issue "Genotype× Environment Interactions in Crop Breeding"

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 9 April 2021.

Special Issue Editors

Dr. Catalina Egea-Gilabert
Website
Guest Editor
Department of Agricultural Engineering, Technical University of Cartagena, Paseo Alfonso XIII, 48, 30203 Cartagena, Spain
Interests: biochemistry; genetics and molecular biology; agricultural and biological sciences
Dr. Mario A. Pagnotta
Website
Guest Editor
Department of Sciences and Technology for Agriculture, Forest, Environment and Energy, Università degli Studi della Tuscia, 01100 Viterbo, Italy
Interests: plant population genetics; plant evolution and domestication; in situ and ex situ conservation of plant germplasm; molecular characterization; molecular markers; molecular evolution; plant breeding
Special Issues and Collections in MDPI journals
Dr. Pasquale Tripodi
Website1 Website2
Guest Editor
Research Centre for Vegetable and Ornamental crops, Council for Agricultural Research and Agricultural Economy Analysis (CREA), Via Cavalleggeri 25, I-84098 Salerno, Italy
Interests: plant breeding and genetics; plant genomics; quantitative genetics; plant phenomics; vegetable quality; solanaceae; leafy vegetables

Special Issue Information

Dear Colleagues,

The main challenges for crop improvement linked to demographic trends of next decades and climate changes require a more efficient use of plant genetic resources in breeding programs aimed at developing more stable varieties. The history of agriculture and, therefore, that of plant breeding, is the history of continuous adaptation to the environment. Genotype x environment interactions (GEI), leading to inconsistency of best-yielding material across cropping environments, challenges plant breeders and complicates cultivar recommendation. Breeders have to test their material in multi-environments, choosing carefully the ones on which their varieties will be cultivated. The GEI occurs when, in a manner analogous to any other factorial experiment, the differences between genotypes depend on the environment in which they are tested. The presence of GEI represents an important challenge for the breeder as, on the one hand, it reduces the genetic advance of the programs by reducing the genotype-phenotype correspondence, although it also allows the identification of ecological niches for which certain genotypes can present specific adaptation. However, it may also offer opportunities, e.g., raising yields through material specifically adapted to a given area or crop management practice, or limiting yield reduction in unfavourable years through the cultivation of stable-yielding material.

For this Special Issue, we welcome original research articles focusing on:

- GEI that targets any agronomic trait of interest in crops with the aim of reaching a more sustainable agriculture;

- Evaluation of agronomic and qualitative performances of crops across multisites;

- Biotic and abiotic stress response in plants in changing environments;

- Statistical approaches for the analysis of the G × E interaction;

- G × E in association mapping studies and genomic selection.

Dr. Catalina Egea-Gilabert
Dr. Mario A. Pagnotta
Dr. Pasquale Tripodi
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • genotype by environment interaction
  • breeding programme
  • product quality
  • cropping systems
  • climate change mitigation
  • high yield potential
  • biotic and abiotic stress
  • traits stability
  • landraces
  • local varieties
  • adaptation
  • phenotypic plasticity
  • statistical models
  • prediction models
  • association mapping studies
  • genomic selection

Published Papers (8 papers)

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Research

Open AccessArticle
Broomrape as a Major Constraint for Grass Pea (Lathyrus sativus) Production in Mediterranean Rain-Fed Environments
Agronomy 2020, 10(12), 1931; https://doi.org/10.3390/agronomy10121931 - 08 Dec 2020
Abstract
Grass pea (Lathyrus sativus) is an annual legume crop that is currently underutilized but has the potential for reintroduction into Mediterranean rain-fed farming systems. In this study, we compared the adaptation of breeding lines in multi-environment field testing, which had wide [...] Read more.
Grass pea (Lathyrus sativus) is an annual legume crop that is currently underutilized but has the potential for reintroduction into Mediterranean rain-fed farming systems. In this study, we compared the adaptation of breeding lines in multi-environment field testing, which had wide variation for precocity, grain yield and broomrape infection. Heritability-adjusted genotype plus genotype-by-environment interaction (HA-GGE) biplot and non-metric multidimensional scaling (NMDS) were performed to determine the effect on genotype (G), environment (E) and G × E interaction on grain yield, precocity and broomrape infection. Precocity was associated with reduced broomrape infection, and this with increased grain yield. Step-wise regression analysis revealed that the broomrape infection had the highest influence on grain yield, whereas precocity had a lower effect. Rain and humidity and mild temperatures before and during flowering were the climatic factors most influential on broomrape. Accessions with a shorter growth cycle suffered lower broomrape infection and were more productive in the environments with a high broomrape incidence. Accessions with longer growth cycle suffered overall higher broomrape infection and were therefore more productive in the environments with low or moderate broomrape incidence. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Open AccessArticle
Variation of Phenotypic Traits in Twelve Bambara Groundnut (Vigna subterranea (L.) Verdc.) Genotypes and Two F2 Bi-Parental Segregating Populations
Agronomy 2020, 10(10), 1451; https://doi.org/10.3390/agronomy10101451 - 23 Sep 2020
Abstract
Underutilised species such as bambara groundnut (Vigna subterranea (L.) Verdc.) have the potential to contribute significantly to meeting food and nutritional needs worldwide. We evaluated phenotypic traits in twelve bambara groundnut genotypes from East, West and Southern Africa and Southeast Asia and [...] Read more.
Underutilised species such as bambara groundnut (Vigna subterranea (L.) Verdc.) have the potential to contribute significantly to meeting food and nutritional needs worldwide. We evaluated phenotypic traits in twelve bambara groundnut genotypes from East, West and Southern Africa and Southeast Asia and two F2 bi-parental segregating populations derived from IITA-686 ×Tiga Nicuru and S19-3 ×DodR to determine phenotypic trait variation and their potential contribution to the development of improved crop varieties. All phenotypic traits in twelve genotypes were significantly influenced (p < 0.01) by genotypes. Principal component analysis (PCA) showed that PC1 accounted for 97.33% variation and was associated with four genotypes collected from East and Southern Africa. PC2 accounted for 2.48% of the variation and was associated with five genotypes collected from East, West and Southern Africa. Transgressive segregation for a number of traits was observed in the two F2 bi-parental populations, as some individual lines in the segregating populations showed trait values greater or less than their parents. The variability between twelve genotypes and the two F2 bi-parental segregating populations and the negative relationship between plant architectural traits and yield related traits provide resources for development of structured populations and breeding lines for bambara groundnut breeding programme. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Open AccessArticle
Stability of Fruit Quality Traits of Different Strawberry Varieties under Variable Environmental Conditions
Agronomy 2020, 10(9), 1242; https://doi.org/10.3390/agronomy10091242 - 23 Aug 2020
Abstract
Strawberry fruit quality traits can be affected by genotype–environment interactions, determining the final consumer acceptance of fruits. Trait stability under varying environments is necessary to ensure the fruit quality of strawberries selected by breeding programs. Hence, inter- and intra-annual variation of organoleptic and [...] Read more.
Strawberry fruit quality traits can be affected by genotype–environment interactions, determining the final consumer acceptance of fruits. Trait stability under varying environments is necessary to ensure the fruit quality of strawberries selected by breeding programs. Hence, inter- and intra-annual variation of organoleptic and functional fruit quality parameters of five strawberry varieties throughout four consecutive cropping seasons was analyzed to assess their relative stability. In most varieties, organoleptic parameters showed higher inter-annual stability but greater variability throughout the season, while the reverse was true for the functional quality parameters. Relative humidity and mean and minimum temperatures partially accounted for fruit quality variation but other factors along with the genotype may also have an influence. Among the varieties, ‘Splendor’ displayed greater year-on-year stability in organoleptic parameters, and ‘Sabrina’ and Candonga® showed higher inter- and intra-annual stability on functional fruit quality, respectively. Environmental variation did not affect fruit quality parameters similarly in all strawberry varieties. In ‘Sabrina’ and Candonga® antioxidant capacity (TEAC) was greater and stable throughout the cropping season, underlining TEAC as a tool for varietal selection, and suggesting these two varieties as parents for breeding programs that seek healthy features and high-quality fruits that meet consumer demands. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Open AccessArticle
Plant Yield Efficiency by Homeostasis as Selection Tool at Ultra-Low Density. A Comparative Study with Common Stability Measures in Maize
Agronomy 2020, 10(8), 1203; https://doi.org/10.3390/agronomy10081203 - 16 Aug 2020
Abstract
The study pertains to field experimentation testing seven maize (Zea mays L.) hybrids at four densities, across five locations under normal (NIR) and low-input (LIR) regimes. The main objective was to assess the prognostic value of plant yield efficiency by homeostasis (PYEH) [...] Read more.
The study pertains to field experimentation testing seven maize (Zea mays L.) hybrids at four densities, across five locations under normal (NIR) and low-input (LIR) regimes. The main objective was to assess the prognostic value of plant yield efficiency by homeostasis (PYEH) for breeding purposes at ultra-low plant density to predict hybrid yield potential and stability. PYEH comprises plant yield efficiency (PYE) that reflects the ability of individual plants to exploit resources, and plant yield homeostasis (PYH) that indicates the crop’s ability to evade acquired plant-to-plant variability. The same hybrids were also evaluated for stability by commonly used parametric and non-parametric statistics based on data at low (LCD) and high crop densities (HCD). Hybrid stability focused on potential yield loss due to erratic optimum density (OD). Most methods produced conflicting results regarding hybrid ranking for yield and stability especially at LCD. In contrast, PYEH consistently highlighted high-yielding and stable hybrids, potentially able to reach the attainable crop yield (ACY) inter-seasonally irrespective of crop spacing. Low density is common practice under resource-deficit conditions, so crop adaptation to crop spacing is a viable option to overcome erratic OD that constitutes a root source of crop instability in rainfed maize. The results were further supportive of breeding at ultra-low density to facilitate the identification and selection of superior genotypes, since such conditions promote phenotypic expression and differentiation, and ensure repeatability across diverse environments. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Open AccessArticle
Adaptation of Winter Wheat Cultivars to Different Environments: A Case Study in Poland
Agronomy 2020, 10(5), 632; https://doi.org/10.3390/agronomy10050632 - 30 Apr 2020
Abstract
A proper understanding of cultivar adaptation to different environments is of great relevance in agronomy and plant breeding. As wheat is the most important crop in Poland, with a total of about 22% of the total sown area, the study of its performance [...] Read more.
A proper understanding of cultivar adaptation to different environments is of great relevance in agronomy and plant breeding. As wheat is the most important crop in Poland, with a total of about 22% of the total sown area, the study of its performance in environments with different productivity levels for consequent cultivar recommendation is of major importance. In this paper, we assess the relative performance of winter wheat cultivars in environments with different productivity and propose a method for cultivar recommendation, by considering the information of environmental conditions and drought stress. This is performed in the following steps: (1) calculation of expected wheat productivity, depending on environmental factors, (2) calculation of relative productivity of cultivars in the environments, and (3) recommendation of cultivars of a specific type and range of adaptation. Soil and weather conditions were confirmed as the most important factors affecting winter wheat yield. The weather factors should be considered rather in shorter (e.g., 10 day) than longer (e.g., 60 day) time periods and in relation to growth stages. The ANCOVA model with genotype and management intensity as fixed factors, and soil and weather parameters as covariates was proposed to assess the expected wheat productivity in particular environments and the expected performance of each genotype (cultivar). The recommendation of cultivars for locations of specified productivity was proposed based on the difference between the expected cultivar yield and the mean wheat productivity, and compared with the Polish official cultivar recommendation list. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Open AccessArticle
RNA-seq Reveals Differentially Expressed Genes between Two indica Inbred Rice Genotypes Associated with Drought-Yield QTLs
Agronomy 2020, 10(5), 621; https://doi.org/10.3390/agronomy10050621 - 28 Apr 2020
Cited by 1
Abstract
Two indica inbred rice lines, IR64, a drought-sensitive, and Apo, a moderately drought-tolerant genotype, were exposed to non- (control or unstressed) and water-stress treatments. Leaf samples collected at an early flowering stage were sequenced by RNA-seq. Reads generated were analyzed for differential expression [...] Read more.
Two indica inbred rice lines, IR64, a drought-sensitive, and Apo, a moderately drought-tolerant genotype, were exposed to non- (control or unstressed) and water-stress treatments. Leaf samples collected at an early flowering stage were sequenced by RNA-seq. Reads generated were analyzed for differential expression (DE) implementing various models in baySeq to capture differences in genome-wide transcriptional response under contrasting water regimes. IR64, the drought-sensitive variety consistently exhibited a broader transcriptional response while Apo showed relatively modest transcriptional changes under water-stress conditions across all models implemented. Gene ontology (GO) and KEGG pathway analyses of genes revealed that IR64 showed enhancement of functions associated with signal transduction, protein binding and receptor activity. Apo uniquely showed significant enrichment of genes associated with an oxygen binding function and peroxisome pathway. In general, IR64 exhibited more extensive molecular re-programming, presumably, a highly energy-demanding route to deal with the abiotic stress. Several of these differentially expressed genes (DEGs) were found to co-localize with QTL marker regions previously identified to be associated with drought-yield response, thus, are the most promising candidate genes for further studies. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Open AccessEditor’s ChoiceArticle
Performance of a Set of Eggplant (Solanum melongena) Lines With Introgressions From Its Wild Relative S. incanum Under Open Field and Screenhouse Conditions and Detection of QTLs
Agronomy 2020, 10(4), 467; https://doi.org/10.3390/agronomy10040467 - 27 Mar 2020
Cited by 2
Abstract
Introgression lines (ILs) of eggplant (Solanum melongena) represent a resource of high value for breeding and the genetic analysis of important traits. We have conducted a phenotypic evaluation in two environments (open field and screenhouse) of 16 ILs from the first [...] Read more.
Introgression lines (ILs) of eggplant (Solanum melongena) represent a resource of high value for breeding and the genetic analysis of important traits. We have conducted a phenotypic evaluation in two environments (open field and screenhouse) of 16 ILs from the first set of eggplant ILs developed so far. Each of the ILs carries a single marker-defined chromosomal segment from the wild eggplant relative S. incanum (accession MM577) in the genetic background of S. melongena (accession AN-S-26). Seventeen agronomic traits were scored to test the performance of ILs compared to the recurrent parent and of identifying QTLs for the investigated traits. Significant morphological differences were found between parents, and the hybrid was heterotic for vigour-related traits. Despite the presence of large introgressed fragments from a wild exotic parent, individual ILs did not display differences with respect to the recipient parent for most traits, although significant genotype × environment interaction (G × E ) was detected for most traits. Heritability values for the agronomic traits were generally low to moderate. A total of ten stable QTLs scattered across seven chromosomes was detected. For five QTLs, the S. incanum introgression was associated with higher mean values for plant- and flower-related traits, including vigour prickliness and stigma length. For one flower- and four fruit-related-trait QTLs, including flower peduncle and fruit pedicel lengths and fruit weight, the S. incanum introgression was associated with lower mean values for fruit-related traits. Evidence of synteny to other previously reported in eggplant populations was found for three of the fruit-related QTLs. The other seven stable QTLs are new, demonstrating that eggplant ILs are of great interest for eggplant breeding under different environments. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Open AccessArticle
Insights into the Genetic Architecture of Phenotypic Stability Traits in Winter Wheat
Agronomy 2020, 10(3), 368; https://doi.org/10.3390/agronomy10030368 - 07 Mar 2020
Cited by 1
Abstract
Examining the architecture of traits through genomics is necessary to gain a better understanding of the genetic loci affecting important traits to facilitate improvement. Genomewide association study (GWAS) and genomic selection (GS) were implemented for grain yield, heading date, and plant height to [...] Read more.
Examining the architecture of traits through genomics is necessary to gain a better understanding of the genetic loci affecting important traits to facilitate improvement. Genomewide association study (GWAS) and genomic selection (GS) were implemented for grain yield, heading date, and plant height to gain insights into the genetic complexity of phenotypic stability of traits in a diverse population of US Pacific Northwest winter wheat. Analysis of variance using the Additive Main Effect and Multiplicative Interaction (AMMI) approach revealed significant genotype and genotype by environment interactions. GWAS identified 12 SNP markers distributed across 10 chromosomes affecting variation for both trait and phenotypic stability, indicating potential pleiotropic effects and signifying that similar genetic loci could be associated with different aspects of stability. The lack of stable and major effect loci affecting phenotypic variation supports the complexity of stability of traits. Accuracy of GS was low to moderate, between 0.14 and 0.66, indicating that phenotypic stability is under genetic control. The moderate to high correlation between trait and trait stability suggests the potential of simultaneous selection for trait and trait stability. Our results demonstrate the complex genetic architecture of trait stability and show the potential for improving stability in winter wheat using genomic-assisted approaches. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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