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: closed (30 April 2021).

Special Issue Editors

Prof. Dr. Catalina Egea-Gilabert
E-Mail 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
E-Mail 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, Collections and Topics in MDPI journals
Dr. Pasquale Tripodi
E-Mail 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 2000 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 (15 papers)

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Editorial

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Editorial
Genotype × Environment Interactions in Crop Breeding
Agronomy 2021, 11(8), 1644; https://doi.org/10.3390/agronomy11081644 - 18 Aug 2021
Viewed by 475
Abstract
In the next decades, the agricultural systems will deal with major challenges linked to the expected population growth, climate changes and necessity of sustainable use of resources able to preserve the environment [...] Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)

Research

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Article
Development of Novel Blackgram (Vigna mungo (L.) Hepper) Mutants and Deciphering Genotype × Environment Interaction for Yield-Related Traits of Mutants
Agronomy 2021, 11(7), 1287; https://doi.org/10.3390/agronomy11071287 - 24 Jun 2021
Cited by 2 | Viewed by 657
Abstract
Blackgram (Vigna mungo (L.) Hepper) yields are noticeably poor due to a shortage of improved varieties and an aggravated narrow genetic base. An attempt was made to isolate novel blackgram mutants by selecting for yield-related traits derived through gamma irradiation and testing [...] Read more.
Blackgram (Vigna mungo (L.) Hepper) yields are noticeably poor due to a shortage of improved varieties and an aggravated narrow genetic base. An attempt was made to isolate novel blackgram mutants by selecting for yield-related traits derived through gamma irradiation and testing the mutant genotype’s stability across the different environments. The irradiated blackgram populations M1-M5 were established in the background of cultivars ADT 3, Co 6, and TU 17-9. Desirable mutants were selected from M3 to M5 generations. It was observed in M2 and M3 that gamma rays showed higher mutagenic efficacy and generated good inherited variance for the yield-related traits. M4 established three divergent groups in each blackgram cultivar revealed by clustering analysis. The number of pods per plant, number of clusters per plant, and number of pods per cluster showed a strong direct association with single plant yield and could be considered as selection traits. G × E interactions were higher than the variation due to genotype for single plant yield. Limited environmental interaction was observed for the genotypes G24, G16, G36, G30, and G17, as revealed by AMMI, and the genotypes G18 and G29, as revealed by GGE. GGE biplot revealed the environment-specific genotypes G13 for E1 (Aduthurai), G7 for E2 (Kattuthottam), and G34 for E3 (Vamban) and also portrayed the highly discriminating (E3) and representative (E2) environments. Selected novel blackgram genotypes from this research are useful genetic stocks for genetic improvement and breeding. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Article
Impact of Fungicide Application and Host Genotype on Susceptibility of Brassica napus to Sclerotinia Stem Rot across the South-Western Australian Grain Belt: A Genotype × Environment × Management Study
Agronomy 2021, 11(6), 1170; https://doi.org/10.3390/agronomy11061170 - 08 Jun 2021
Cited by 1 | Viewed by 783
Abstract
Sclerotinia stem rot (SSR), caused by the necrotroph Sclerotinia sclerotiorum Lib. (de Bary), is a major disease of canola in Australia, greatly reducing yields in high infection years. This study investigated genotype by environment by management interactions at 25 sites across the south-west [...] Read more.
Sclerotinia stem rot (SSR), caused by the necrotroph Sclerotinia sclerotiorum Lib. (de Bary), is a major disease of canola in Australia, greatly reducing yields in high infection years. This study investigated genotype by environment by management interactions at 25 sites across the south-west Australian grainbelt from 2017 to 2020. Up to 10 canola varieties were grown each year with +/− fungicide application at 30% flowering. Disease incidence was low, with less than 20% infection recorded across most sites. Most variation in yield occurred between sites, rather than by management or variety, due to the environmental differences between the sites. Petal assays were found to be a poor indicator of later disease severity, suggesting the winter growing season in south-west Australia does not have reliable conducive conditions for disease development following petal drop in canola. The Additive Main Effects and Multiplicative Interaction model (AMMI) indicated that the open-pollinated varieties were broadly adapted and stable when fungicide was applied but became unstable with no fungicide, indicating SSR has a significant impact on yield when disease incidence is higher. This study highlights that further research is necessary to determine disease thresholds that lead to significant yield loss. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Article
Genomic Prediction and Genotype-by-Environment Interaction Analysis of Crown and Stem Rust in Ryegrasses in European Multi-Site Trials
Agronomy 2021, 11(6), 1119; https://doi.org/10.3390/agronomy11061119 - 30 May 2021
Cited by 1 | Viewed by 968
Abstract
Climate change calls for novel approaches to include environmental effects in future breeding programs for forage crops. A set of ryegrasses (Lolium) varieties was evaluated in multiple European environments for crown rust (Puccinia coronata f. sp. lolii) and stem [...] Read more.
Climate change calls for novel approaches to include environmental effects in future breeding programs for forage crops. A set of ryegrasses (Lolium) varieties was evaluated in multiple European environments for crown rust (Puccinia coronata f. sp. lolii) and stem rust (P. graminis f. sp. graminicola) resistance. Additive Main Effect and Multiplicative Interaction (AMMI) analysis revealed significant genotype (G) and environment (E) effects as well as the interaction of both factors (G × E). Genotypes plus Genotype-by-Environment interaction (GGE) analysis grouped the tested environments in multiple mega-environments for both traits suggesting the presence of an environmental effect on the ryegrasses performances. The best performing varieties in the given mega-environments showed high resistance to crown as well as stem rust, and overall, tetraploid varieties performed better than diploid. Furthermore, we modeled G × E using a marker x environment interaction (M × E) model to predict the performance of varieties tested in some years but not in others. Our results showed that despite the limited number of varieties, the high number of observations allowed us to predict both traits’ performances with high accuracy. The results showed that genomic prediction using multi environmental trials could enhance breeding programs for the crown and stem rust in ryegrasses. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Article
Energy Cane x Sugarcane Microregion Interaction in the State of Pernambuco: Sugarcane for Production of Bioenergy and Renewable Fuels
Agronomy 2021, 11(6), 1046; https://doi.org/10.3390/agronomy11061046 - 24 May 2021
Cited by 1 | Viewed by 581
Abstract
Assessing the differential behavior of a group of genotypes in various environments is fundamentally important in any breeding program. As sugarcane is the most important crop in the state of Pernambuco, it is of great relevance to study its performance in different cultivation [...] Read more.
Assessing the differential behavior of a group of genotypes in various environments is fundamentally important in any breeding program. As sugarcane is the most important crop in the state of Pernambuco, it is of great relevance to study its performance in different cultivation sites to assist in the recommendation of new cultivars that increase the productivity of the cane fields. In view of the new demand from the sugar-energy sector for cultivars with high energy potential, this work aimed to select and recommend new genotypes with high fiber and sucrose percentage in the sugarcane microregions of the state of Pernambuco. The methodologies used to classify genotypes for adaptability and stability were as follows: simple linear regression, the modified centroid method, additive main effects, multiplicative interaction analysis, and linear mixed models. Genotypes with higher productivity and specific adaptability to the tested microregions were identified. The methodologies applied were efficient and complementary in recommending genotypes with favorable prospects for increasing sugar productivity, cogeneration of electric energy and the production of renewable fuels. Genotypes 6, 7, 9, 14, 16, and 18 stand out in terms of the productivity of sugar and fiber, with high potential to be released as commercial cultivars. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Article
Implementation of a Generalized Additive Model (GAM) for Soybean Maturity Prediction in African Environments
Agronomy 2021, 11(6), 1043; https://doi.org/10.3390/agronomy11061043 - 22 May 2021
Cited by 1 | Viewed by 1125
Abstract
Time to maturity (TTM) is an important trait in soybean breeding programs. However, soybeans are a relatively new crop in Africa. As such, TTM information for soybeans is not yet as well defined as in other major producing areas. Multi-environment trials (METs) allow [...] Read more.
Time to maturity (TTM) is an important trait in soybean breeding programs. However, soybeans are a relatively new crop in Africa. As such, TTM information for soybeans is not yet as well defined as in other major producing areas. Multi-environment trials (METs) allow breeders to analyze crop performance across diverse conditions, but also pose statistical challenges (e.g., unbalanced data). Modern statistical methods, e.g., generalized additive models (GAMs), can flexibly smooth a range of responses while retaining observations that could be lost under other approaches. We leveraged 5 years of data from an MET breeding program in Africa to identify the best geographical and seasonal variables to explain site and genotypic differences in soybean TTM. Using soybean cycle features (e.g., minimum temperature, daylength) along with trial geolocation (longitude, latitude), a GAM predicted soybean TTM within 10 days of the average observed TTM (RMSE = 10.3; x = 109 days post-planting). Furthermore, we found significant differences between cultivars (p < 0.05) in TTM sensitivity to minimum temperature and daylength. Our results show potential to advance the design of maturity systems that enhance soybean planting and breeding decisions in Africa. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Article
Phenotypic and Quality Traits of Chickpea Genotypes under Rainfed Conditions in South Italy
Agronomy 2021, 11(5), 962; https://doi.org/10.3390/agronomy11050962 - 12 May 2021
Cited by 5 | Viewed by 755
Abstract
Chickpea (Cicer arietinum L.) is an important cool-season food legume crop that is mainly cultivated as a rainfed crop. This study was conducted in Italy between 2017 and 2019 to evaluate the stability of seed yield (SY), biomass (AGB) and 1000 seed [...] Read more.
Chickpea (Cicer arietinum L.) is an important cool-season food legume crop that is mainly cultivated as a rainfed crop. This study was conducted in Italy between 2017 and 2019 to evaluate the stability of seed yield (SY), biomass (AGB) and 1000 seed weight (THS), and to assess the seed quality of 12 kabuli chickpea accessions under field conditions. The likelihood-ratio test revealed significant effects of genotype only for the SY and THS. The environment and genotype × environment interaction (GEI) effects were highly significant for all variables. We found that the environment (year) and GEI explain 55.72% and 20.87% of the total seed yield variation, respectively. Most chickpea accessions showed sensitivity to frost conditions in the third growing season. No relationship was observed between the yield and the protein content in Kabuli chickpea. Among the accessions, Ares and Reale showed the best performance under all environmental conditions, and the Reale was the most stable chickpea. Full article
(This article belongs to the Special Issue Genotype× Environment Interactions in Crop Breeding)
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Article
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
Cited by 4 | Viewed by 797
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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Article
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
Cited by 2 | Viewed by 993
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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Article
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
Cited by 10 | Viewed by 1072
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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Article
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
Cited by 1 | Viewed by 1334
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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Article
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
Cited by 8 | Viewed by 1039
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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Article
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 7 | Viewed by 1729
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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Article
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 9 | Viewed by 1913
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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Article
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 11 | Viewed by 1267
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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