scholarly journals Single-gene resolution of locally adaptive genetic variation in Mexican maize

2019 ◽  
Author(s):  
Daniel J Gates ◽  
Dan Runcie ◽  
Garrett M. Janzen ◽  
Alberto Romero Navarro ◽  
Martha Willcox ◽  
...  
Keyword(s):  
Crop Production ◽  
Agronomic Traits ◽  
Single Gene ◽  
Crop Wild Relatives ◽  
Plant Performance ◽  
Ex Situ ◽  
Environment Interaction ◽  
Genetic Associations ◽  
Adaptive Genetic Variation ◽  
Traditional Landraces

AbstractThreats to crop production due to climate change are one of the greatest challenges facing plant breeders today. While considerable adaptive variation exists in traditional landraces, natural populations of crop wild relatives, and ex situ germplasm collections, separating adaptive alleles from linked deleterious variants that impact agronomic traits is challenging and has limited the utility of these diverse germplasm resources. Modern genome editing techniques such as CRISPR offer a potential solution by targeting specific alleles for transfer to new backgrounds, but such methods require a higher degree of precision than traditional mapping approaches can achieve. Here we present a high-resolution genome-wide association analysis to identify loci exhibiting adaptive patterns in a large panel of more than 4500 traditional maize landraces representing the breadth of genetic diversity of maize in Mexico. We evaluate associations between genotype and plant performance in 13 common gardens across a range of environments, identifying hundreds of candidate genes underlying genotype by environment interaction. We further identify genetic associations with environment across Mexico and show that such loci are associated with variation in yield and flowering time in our field trials and predict performance in independent drought trials. Our results indicate that the variation necessary to adapt crops to changing climate exists in traditional landraces that have been subject to ongoing environmental adaptation and can be identified by both phenotypic and environmental association.

Epistatic Effects and QTL×Environment Interaction Effects of QTLs for Yield and Agronomic Traits in Soybean

2014 ◽  
Vol 40 (1) ◽  
pp. 37
Author(s):  
Hui-Zhen LIANG ◽  
Yong-Liang YU ◽  
Hong-Qi YANG ◽  
Hai-Yang ZHANG ◽  
Wei DONG ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Interaction Effects ◽  
Environment Interaction ◽  
Epistatic Effects

scholarly journals Fungicide Application Affects Nitrogen Utilization Efficiency, Grain Yield, and Quality of Winter Wheat

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1295
Author(s):  
Ahossi Patrice Koua ◽  
Mirza Majid Baig ◽  
Benedict Chijioke Oyiga ◽  
Jens Léon ◽  
Agim Ballvora
Keyword(s):  
Synergistic Effect ◽  
Grain Yield ◽  
Crop Production ◽  
Agronomic Traits ◽  
Yellow Rust ◽  
Wheat Yield ◽  
Utilization Efficiency ◽  
High Nitrogen ◽  
Available N ◽  
Fungicide Application

Nitrogen (N) is a vital component of crop production. Wheat yield varies significantly under different soil available N. Knowing how wheat responds to or interacts with N to produce grains is essential in the selection of N use efficient cultivars. We assessed in this study variations among wheat genotypes for productivity-related traits under three cropping systems (CS), high-nitrogen with fungicide (HN-WF), high-nitrogen without fungicide (HN-NF) and low-nitrogen without fungicide (LN-NF) in the 2015, 2016 and 2017 seasons. ANOVA results showed genotypes, CS, and their interactions significantly affected agronomic traits. Grain yield (GY) increased with higher leaf chlorophyll content, importantly under CS without N and fungicide supply. Yellow rust disease reduced the GY by 20% and 28% in 2015 and 2016, respectively. Moreover, averaged over growing seasons, GY was increased by 23.78% under CS with N supply, while it was greatly increased, by 52.84%, under CS with both N and fungicide application, indicating a synergistic effect of N and fungicide on GY. Fungicide supply greatly improved the crop ability to accumulate N during grain filling, and hence the grain protein content. Recently released cultivars outperformed the older ones in most agronomic traits including GY. Genotype performance and stability analysis for GY production showed differences in their stability levels under the three CS. The synergistic effect of nitrogen and fungicide on grain yield (GY) and the differences in yield stability levels of recently released wheat cultivars across three CS found in this study suggest that resource use efficiency can be improved via cultivar selection for targeted CS.

scholarly journals Meta-QTL analysis and identification of candidate genes for quality, abiotic and biotic stress in durum wheat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jose Miguel Soriano ◽  
Pasqualina Colasuonno ◽  
Ilaria Marcotuli ◽  
Agata Gadaleta
Keyword(s):  
Molecular Markers ◽  
Abiotic Stress ◽  
Durum Wheat ◽  
Candidate Genes ◽  
Biotic Stress ◽  
Qtl Analysis ◽  
Complex Traits ◽  
Genetic Basis ◽  
Agronomic Traits ◽  
Plant Performance

AbstractThe genetic improvement of durum wheat and enhancement of plant performance often depend on the identification of stable quantitative trait loci (QTL) and closely linked molecular markers. This is essential for better understanding the genetic basis of important agronomic traits and identifying an effective method for improving selection efficiency in breeding programmes. Meta-QTL analysis is a useful approach for dissecting the genetic basis of complex traits, providing broader allelic coverage and higher mapping resolution for the identification of putative molecular markers to be used in marker-assisted selection. In the present study, extensive QTL meta-analysis was conducted on 45 traits of durum wheat, including quality and biotic and abiotic stress-related traits. A total of 368 QTL distributed on all 14 chromosomes of genomes A and B were projected: 171 corresponded to quality-related traits, 127 to abiotic stress and 71 to biotic stress, of which 318 were grouped in 85 meta-QTL (MQTL), 24 remained as single QTL and 26 were not assigned to any MQTL. The number of MQTL per chromosome ranged from 4 in chromosomes 1A and 6A to 9 in chromosome 7B; chromosomes 3A and 7A showed the highest number of individual QTL (4), and chromosome 7B the highest number of undefined QTL (4). The recently published genome sequence of durum wheat was used to search for candidate genes within the MQTL peaks. This work will facilitate cloning and pyramiding of QTL to develop new cultivars with specific quantitative traits and speed up breeding programs.

scholarly journals Status of the Ex Situ and In Situ Conservation of Brazilian Crop Wild Relatives of Rice, Potato, Sweet Potato, and Finger Millet: Filling the Gaps of Germplasm Collections

Agronomy ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 638
Author(s):  
Marcelo B. Medeiros ◽  
José F. M. Valls ◽  
Aluana G. Abreu ◽  
Gustavo Heiden ◽  
Suelma Ribeiro-Silva ◽  
...  
Keyword(s):  
Finger Millet ◽  
Ex Situ Conservation ◽  
Gap Analysis ◽  
In Situ Conservation ◽  
Germplasm Collection ◽  
Crop Wild Relatives ◽  
Wild Relatives ◽  
Ex Situ ◽  
The Status

This study presents the status of ex situ and in situ conservation for the crop wild relatives of rice, potato, sweet potato, and finger millet in Brazil, and the subsequent germplasm collection expeditions. This research is part of a global initiative entitled “Adapting Agriculture to Climate Change: Collecting, Protecting, and Preparing Crop Wild Relatives” supported by the Global Crop Diversity Trust. Species of the primary, secondary, and tertiary gene pools with occurrences reported in Brazil were included: Oryza alta Swallen, O. grandiglumis (Döll) Prod., O. latifolia Desv., O. glumaepatula Steud., Eleusine tristachya (Lam.) Lam., E. indica (L.) Gaertn., Solanum commersonii Dunal, S. chacoense Bitter, Ipomoea grandifolia (Dammer) O’Donell, I. ramosissima (Poir.) Choisy, I. tiliacea (Willd.) Choisy, I. triloba L., and I. cynanchifolia Meisn. The status of the ex situ and in situ conservation of each taxon was assessed using the gap analysis methodology, and the results were used to plan 16 germplasm collection expeditions. Seeds of the collected material were evaluated for viability, and the protocols for seed germination and cryopreservation were tested. The final conservation score, resulting from the gap analysis and including the average of the ex situ and in situ scores, resulted in a classification of medium priority of conservation for all the species, with the exception of I. grandifolia (high priority). The total accessions collected (174) almost doubled the total accessions of these crop wild relatives incorporated in Embrapa’s ex situ conservation system prior to 2015. In addition, accessions for practically absent species were collected for the ex situ conservation system, such as Ipomoea species, Eleusine indica, and Solanum chacoense. The methods used for dormancy breaking and low temperature conservation for the Oryza, Eleusine, and Ipomoea species were promising for the incorporation of accessions in the respective gene banks. The results show the importance of efforts to collect and conserve ex situ crop wild relatives in Brazil based on previous gap analysis. The complementarity with the in situ strategy also appears to be very promising in the country.

Stability Analysis of Agronomic Traits for Maize (Zea Mays L.) Genotypes Based on Ammi Model

2021 ◽  
Vol 50 (2) ◽  
pp. 343-350
Author(s):  
Meijin Ye ◽  
Zhaoyang Chen ◽  
Bingbing Liu ◽  
Haiwang Yue
Keyword(s):  
Grain Yield ◽  
Agronomic Traits ◽  
Interaction Model ◽  
Genotype By Environment Interaction ◽  
Kernel Weight ◽  
Environment Interaction ◽  
Maize Hybrids ◽  
Genotype By Environment ◽  
Ammi Model ◽  
The Ideal

Stability and adaptability of promising maize hybrids in terms of three agronomic traits (grain yield, ear weight and 100-kernel weight) in multi-environments trials were evaluated. The analysis of AMMI model indicated that the all three agronomic traits showed highly significant differences (p < 0.01) on genotype, environment and genotype by environment interaction. Results showed that genotypes Hengyu321 (G9), Yufeng303 (G10) and Huanong138 (G3) were of higher stability on grain yield, ear weight and 100-kernel weight, respectively. Genotypes Hengyu1587 (G8) and Hengyu321 (G9) showed good performance in terms of grain yield, whereas Longping208 (G2) and Weike966 (G12) showed broad adaptability for ear weight. It was also found that the genotypes with better adaptability in terms of 100-kernel weight were Zhengdan958 (G5) and Weike966 (G12). The genotype and environment interaction model based on AMMI analysis indicated that Hengyu1587 and Hengyu321 were the ideal genotypes, due to extensive adaptability and high grain yield under both testing sites. Bangladesh J. Bot. 50(2): 343-350, 2021 (June)

scholarly journals Canaryseed (Phalaris canariensis L.) accessions from nineteen countries show useful genetic variation for agronomic traits

2011 ◽  
Vol 91 (1) ◽  
pp. 37-48 ◽  
Author(s):  
M. Cogliatti ◽  
F. Bongiorno ◽  
H. Dalla Valle ◽  
W J Rogers
Keyword(s):  
Genetic Variation ◽  
Grain Yield ◽  
Harvest Index ◽  
Agronomic Traits ◽  
Grain Weight ◽  
Environment Interaction ◽  
Grain Number ◽  
Harvest Maturity ◽  
Phalaris Canariensis ◽  
Late Sowing

Fifty-seven accessions of canaryseed (47 populations and 10 cultivars) from 19 countries were evaluated for agronomic traits in four field trials sown over 3 yr in the province of Buenos Aires, Argentina. Genetic variation was found for all traits scored: grain yield and its components (grain weight, grain number per square meter, grain number per head and head number per square meter), harvest index, percent lodging, and phenological characters (emergence to heading, emergence to harvest maturity and heading to harvest maturity). Although genotype × environment interaction was observed for all traits, the additive differences between accessions were sufficient to enable promising breeding materials to be identified. Accessions superior in performance to the local Argentinean population, which in general gave values close to the overall mean of the accessions evaluated, were identified. For example, a population of Moroccan origin gave good yield associated with elevated values of the highly heritable character grain weight, rather than with the more commonly observed grain number per square meter. This population was also of relatively short stature and resistant to lodging, and, although it performed best when sown within the normal sowing date, tolerated late sowing fairly well. Other accessions were also observed with high grain weight, a useful characteristic in itself, since large grains are desirable from a quality point of view. Regarding phenology, the accessions showed a range of 160 degree days (8 calendar days in our conditions) in maturity, which, while not large in magnitude, may be of some utility in crop rotation management. Some accessions were well adapted to late sowing. Grain yield in general was strongly correlated with grain number per square meter. Principal components analysis (PCA) carried out for all characteristics provided indications of accessions combining useful characteristics and identified three components that explained approximately 70% of the phenotypic variation. Furthermore, a second PCA plus regression showed that approximately 60% of the variation in grain yield could be explained by a component associated with harvest index and grain number per square meter. Pointers were provided to possible future breeding targets.Key words: Phalaris canariensis, canaryseed, accessions, yield, phenology, genetics, breeding

scholarly journals In vitro performance in cotton plants with different genetic backgrounds: the case of Gossypium hirsutum in Mexico, and its implications for germplasm conservation

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7017 ◽  
Author(s):  
Alejandra Hernández-Terán ◽  
Ana Wegier ◽  
Mariana Benítez ◽  
Rafael Lira ◽  
Tania Gabriela Sosa Fuentes ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Biodiversity Conservation ◽  
Crop Production ◽  
Statistical Tests ◽  
Germplasm Conservation ◽  
Ex Situ ◽  
Conservation Strategies ◽  
Wild Germplasm ◽  
Wild Cotton

One of the best ex situ conservation strategies for wild germplasm is in vitro conservation of genetic banks. The success of in vitro conservation relies heavily on the micropropagation or performance of the species of interest. In the context of global change, crop production challenges and climate change, we face a reality of intensified crop production strategies, including genetic engineering, which can negatively impact biodiversity conservation. However, the possible consequences of transgene presence for the in vitro performance of populations and its implications for biodiversity conservation are poorly documented. In this study we analyzed experimental evidence of the potential effects of transgene presence on the in vitro performance of Gossypium hirsutum L. populations, representing the Mexican genetic diversity of the species, and reflect on the implications of such presence for ex situ genetic conservation of the natural variation of the species. We followed an experimental in vitro performance approach, in which we included individuals from different wild cotton populations as well as individuals from domesticated populations, in order to differentiate the effects of domestication traits dragged into the wild germplasm pool via gene flow from the effects of transgene presence. We evaluated the in vitro performance of five traits related to plant establishment (N = 300): propagation rate, leaf production rate, height increase rate, microbial growth and root development. Then we conducted statistical tests (PERMANOVA, Wilcoxon post-hoc tests, and NMDS multivariate analyses) to evaluate the differences in the in vitro performance of the studied populations. Although direct causality of the transgenes to observed phenotypes requires strict control of genotypes, the overall results suggest detrimental consequences for the in vitro culture performance of wild cotton populations in the presence of transgenes. This provides experimental, statistically sound evidence to support the implementation of transgene screening of plants to reduce time and economic costs in in vitro establishment, thus contributing to the overarching goal of germplasm conservation for future adaptation.

scholarly journals Deciphering Main Climate and Edaphic Components Driving Oat Adaptation to Mediterranean Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Francisco J. Canales ◽  
Gracia Montilla-Bascón ◽  
Luis M. Gallego-Sánchez ◽  
Fernando Flores ◽  
Nicolas Rispail ◽  
...  
Keyword(s):  
Environmental Variables ◽  
Agronomic Traits ◽  
Interaction Analysis ◽  
Variation Partitioning ◽  
Environment Interaction ◽  
Edaphic Factors ◽  
Mediterranean Environments ◽  
Wide Range ◽  
Northern Regions ◽  
Edaphic Variables

Oat, Avena sativa, is an important crop traditionally grown in cool-temperate regions. However, its cultivated area in the Mediterranean rim steadily increased during the last 20 years due to its good adaptation to a wide range of soils. Nevertheless, under Mediterranean cultivation conditions, oats have to face high temperatures and drought episodes that reduce its yield as compared with northern regions. Therefore, oat crop needs to be improved for adaptation to Mediterranean environments. In this work, we investigated the influence of climatic and edaphic variables on a collection of 709 Mediterranean landraces and cultivars growing under Mediterranean conditions. We performed genotype–environment interaction analysis using heritability-adjusted genotype plus genotype–environment biplot analyses to determine the best performing accessions. Further, their local adaptation to different environmental variables and the partial contribution of climate and edaphic factors to the different agronomic traits was determined through canonical correspondence, redundancy analysis, and variation partitioning. Here, we show that northern bred elite cultivars were not among the best performing accessions in Mediterranean environments, with several landraces outyielding these. While all the best performing cultivars had early flowering, this was not the case for all the best performing landraces, which showed different patterns of adaption to Mediterranean agroclimatic conditions. Thus, higher yielding landraces showed adaptation to moderate to low levels of rain during pre- and post-flowering periods and moderate to high temperature and radiation during post-flowering period. This analysis also highlights landraces adapted to more extreme environmental conditions. The study allowed the selection of oat genotypes adapted to different climate and edaphic factors, reducing undesired effect of environmental variables on agronomic traits and highlights the usefulness of variation partitioning for selecting genotypes adapted to specific climate and edaphic conditions.

Distinct rhizomicrobiota assemblages and plant performance in lettuce grown in soils with different agricultural management histories

2021 ◽  
Vol 97 (4) ◽  
Author(s):  
Doreen Babin ◽  
Loreen Sommermann ◽  
Soumitra Paul Chowdhury ◽  
Jan H Behr ◽  
Martin Sandmann ◽  
...  
Keyword(s):  
Growth Regulators ◽  
Stress Responses ◽  
Crop Production ◽  
Agricultural Management ◽  
Plant Performance ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Soil Microbiota ◽  
Sustainable Crop Production

ABSTRACT A better understanding of factors shaping the rhizosphere microbiota is important for sustainable crop production. We hypothesized that the effect of agricultural management on the soil microbiota is reflected in the assemblage of the rhizosphere microbiota with implications for plant performance. We designed a growth chamber experiment growing the model plant lettuce under controlled conditions in soils of a long-term field experiment with contrasting histories of tillage (mouldboard plough vs cultivator tillage), fertilization intensity (intensive standard nitrogen (N) + pesticides/growth regulators vs extensive reduced N without fungicides/growth regulators), and last standing field crop (rapeseed vs winter wheat). High-throughput sequencing of bacterial and archaeal 16S rRNA genes and fungal ITS2 regions amplified from total community DNA showed that these factors shaped the soil and rhizosphere microbiota of lettuce, however, to different extents among the microbial domains. Pseudomonas and Olpidium were identified as major indicators for agricultural management in the rhizosphere of lettuce. Long-term extensive fertilization history of soils resulted in higher lettuce growth and increased expression of genes involved in plant stress responses compared to intensive fertilization. Our work adds to the increasing knowledge on how soil microbiota can be manipulated by agricultural management practices which could be harnessed for sustainable crop production.

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