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Agronomy
Special Issues
Analysis of Complex Traits and Molecular Selection in Annual Crops
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Analysis of Complex Traits and Molecular Selection in Annual Crops

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

Deadline for manuscript submissions: closed (15 December 2023) | Viewed by 7327

Special Issue Editors

Dr. Chao Shen

E-Mail Website
Guest Editor
College of Biological and Food Engineering, Guangdong University of Petrochemical Technology, Maoming 525000, China
Interests: genomics; domestication; population genetics; QTL mapping; genome-wide association study; complex traits
Special Issues, Collections and Topics in MDPI journals
Dr. Hantao Wang

E-Mail Website
Guest Editor
State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China
Interests: molecular mechanisms; regulatory network; QTL mapping; genome-wide association study
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Agronomic traits of crops are some of the most concerned issues in agricultural production. The analyses of complex agronomic traits, such as crop yield, quality and stress resistance, molecular selection, and the construction and mining of complex relationship networks between crop genes and agronomic traits, represent the frontiers and hot issues in crop research. Complex agronomic traits of crops are controlled by the effects of multiple genes, environments, gene–gene interactions, and gene–environment interactions. For a long time, there has been a lack of effective research which analyzes complex agronomic traits. With the development of high-throughput sequencing technology, we can comprehensively and systematically understand the composition of complex agronomic traits and molecular selection breeding.

In this Special Issue, we seek integrative studies that highlight the genetic basis of complex agronomic traits in annual crops for molecular selection, including (but not limited to) the development of new techniques and methods and the integration of multiple omics data for the analysis of complex agronomic traits, as well as reviews that offer original perspectives on the analysis of complex traits and molecular selection in annual crops.

Dr. Chao Shen
Dr. Hantao Wang
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 submissions that pass pre-check are 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 2600 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

  • complex traits
  • QTL mapping
  • molecular selection
  • genome-wide association study
  • linkage mapping
  • genomics
  • population genetics
  • domestication and improvement

Related Special Issue

Published Papers (6 papers)

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Editorial

Jump to: Research

5 pages, 186 KiB  
Editorial
Analysis of Complex Traits and Molecular Selection in Annual Crops
by Chao Shen
Agronomy 2024, 14(5), 948; https://doi.org/10.3390/agronomy14050948 - 1 May 2024
Viewed by 403
Abstract
Annual crops, which include staple crops like rice [...] Full article
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops)

Research

Jump to: Editorial

17 pages, 3110 KiB  
Article
Application of a High-Density Single Nucleotide Polymorphism Genetic Map in Mapping Quantitative Trait Loci of Early-Maturing Traits in Upland Cotton
by Guangzhi Mao, Hengling Wei, Pengyun Chen, Feng Xing and Hantao Wang
Agronomy 2023, 13(11), 2716; https://doi.org/10.3390/agronomy13112716 - 28 Oct 2023
Viewed by 935
Abstract
(1) Background: Mapping QTLs for early-maturing traits is necessary for the development of early-maturing variety breeding. (2) Methods: In this research, a high-density genetic map (HDGM) was constructed using an F2 population with 100 individuals and single nucleotide polymorphism markers (SNPs) developed [...] Read more.
(1) Background: Mapping QTLs for early-maturing traits is necessary for the development of early-maturing variety breeding. (2) Methods: In this research, a high-density genetic map (HDGM) was constructed using an F2 population with 100 individuals and single nucleotide polymorphism markers (SNPs) developed using the genotyping-by-sequencing (GBS) method. (3) Results: The HDGM, which covered a total distance of 3167.14 cM, harbored 5454 SNPs with an average marker interval of 0.58 cM. In total, 18 QTLs for four early-maturing characters were detected and explained 11.6–46.4% of phenotypic variation (PV). Two QTLs of the whole growing period (WGP) and height of the node of the first fruiting branch (HNFFB) were identified as stable QTLs. In total, 125 candidate genes were identified in the confidence intervals of these stable QTLs. Presumably, Gh_D03G0857 may play an important role in regulating earliness. (4) Conclusions: This research will provide new information about fine mapping of QTLs for earliness traits, molecular marker assisted selection (MAS) of earliness traits, and pyramiding breeding as well. Full article
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops)
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24 pages, 3579 KiB  
Article
Morphological and Ecogeographical Diversity of the Andean Lupine (Lupinus mutabilis Sweet) in the High Andean Region of Ecuador
by Doris Chalampuente-Flores, María Rosa Mosquera-Losada, Antonio M. De Ron, César Tapia Bastidas and Marten Sørensen
Agronomy 2023, 13(8), 2064; https://doi.org/10.3390/agronomy13082064 - 4 Aug 2023
Viewed by 1740
Abstract
Promoting food security is one of the 17 Sustainable Development Goals (SDGs) proposed by the United Nations General Assembly, with a target date of 2030. Human nutrition based on legume consumption is essential to ensuring food security while reducing greenhouse gas emissions associated [...] Read more.
Promoting food security is one of the 17 Sustainable Development Goals (SDGs) proposed by the United Nations General Assembly, with a target date of 2030. Human nutrition based on legume consumption is essential to ensuring food security while reducing greenhouse gas emissions associated with nitrogen fertilizer use. Moreover, preserving legume biodiversity is critical to increasing agricultural resilience against climate change. The Andean lupine or “tarwi” (Lupinus mutabilis Sweet) is a legume native to the Andean region with high nutritional importance. Morphological characterization processes allow the determination of local agro-biodiversity and the identification of promising materials for genetic improvement programs. In the present investigation, 173 accessions of Andean lupine from the Germplasm Bank of INIAP, Ecuador, were evaluated. Thirteen quantitative and fifteen qualitative descriptors were used in the characterization. The results revealed that the genetic variability of the Andean lupine is represented by the conformation of four groups of accessions. Among those groups, two accessions stand out for having small plants and high yields, factors that could be used for genetic improvement processes or be reintroduced into farmers’ fields as they represent an option for the production, consumption, and marketing of the local germplasm of this relevant ancient crop. A phenotypic diversity map of the cultivated tarwi explained that areas with high morphological diversity are not completely identical to areas with high ecogeographic diversity. The distribution of the genetic variability of species appears to be more related to cultural aspects than environmental conditions. Full article
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops)
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11 pages, 2227 KiB  
Communication
In Vitro Assessment of Salt Stress Tolerance in Wild Potato Species
by Raffaele Garramone, Giuseppe Paolo Coppola, Riccardo Aversano, Teresa Docimo, Petr Sedlák and Domenico Carputo
Agronomy 2023, 13(7), 1784; https://doi.org/10.3390/agronomy13071784 - 30 Jun 2023
Viewed by 1200
Abstract
Proof of concept salt tolerance and plasticity. Wild germplasm may represent a precious source of genetic variability for salt tolerance. This study evaluated the morphological changes occurring under controlled and saline conditions in tuber-bearing S. bulbocastanum, S. commersonii, S. chomatophyllum, [...] Read more.
Proof of concept salt tolerance and plasticity. Wild germplasm may represent a precious source of genetic variability for salt tolerance. This study evaluated the morphological changes occurring under controlled and saline conditions in tuber-bearing S. bulbocastanum, S. commersonii, S. chomatophyllum, S. multidissectum, S. pinnactisectum, S. phureja, and cultivated S. tuberosum. An in vitro screening method was employed. Significant phenotypic variations were observed for all phenotypic traits analyzed at all NaCl levels (0, 40, 60, and 120 mM). In addition, a significant correlation between root plasticity and salt tolerance was found. Further, changes in proline and total phenolic content were assessed to envisage the metabolic adjustments of tolerant clones towards salinity. The most promising sources of tolerance were identified in S. commersonii and S. multidissectum and information obtained is discussed from a breeding perspective. Full article
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops)
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13 pages, 5666 KiB  
Article
Population Genomics Unravels the Characteristic Relationship between Introgression and Geographical Distribution in Upland Cotton
by Chao Shen, Zheng Cao, Zhiyong Xu, Lejun Ouyang, Xumin Zhang, Zhishan Guo, Jieli Yu, Rong Chen and Wenxi Huang
Agronomy 2023, 13(7), 1781; https://doi.org/10.3390/agronomy13071781 - 30 Jun 2023
Cited by 1 | Viewed by 1009
Abstract
Introgression is an important driver of new genetic variation that increases species and genetic diversity. However, the relationship between introgression and geographic distribution of upland cotton is still unclear. Herein, we explored geographically comprehensive genomic data based on 890 upland cotton accessions to [...] Read more.
Introgression is an important driver of new genetic variation that increases species and genetic diversity. However, the relationship between introgression and geographic distribution of upland cotton is still unclear. Herein, we explored geographically comprehensive genomic data based on 890 upland cotton accessions to decipher the degree of introgression between different geographic distributions and its effect on selection and fiber quality. We found introgression intervals to exist across different geographic distributions. Introgression is affected by the similarity of the environment in which they live, and those with similar ecological environments tend to share the same introgression area. Introgression is affected by artificial selection. A genome-wide association study (GWAS) meta-analysis was performed with 6 fiber traits and identified 261 quantitative trait loci (QTLs). We found that 67 QTLs had introgression signals, and the genome interval size was 118.81 Mb, while 123 QTLs had selection signals, and the genomic interval was 28.38 Mb. These results provide insights into the population-scaled introgression landscape, suggesting that introgression contributed to the cotton genetic improvement, which provides a useful reference for studying intraspecific introgressions from different geographical distributions in other species. Full article
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops)
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19 pages, 3795 KiB  
Article
Identification of SNPs Associated with Grain Quality Traits in Spring Barley Collection Grown in Southeastern Kazakhstan
by Yuliya Genievskaya, Shyryn Almerekova, Saule Abugalieva, Aigul Abugalieva, Kazuhiro Sato and Yerlan Turuspekov
Agronomy 2023, 13(6), 1560; https://doi.org/10.3390/agronomy13061560 - 6 Jun 2023
Cited by 4 | Viewed by 1373
Abstract
Barley (Hordeum vulgare L.) is an important cereal crop with high genome plasticity that is cultivated in all climatic zones. Traditionally, barley grain is used for animal feed, malting, brewing, and food production. Depending on the end-use product, there are individual requirements [...] Read more.
Barley (Hordeum vulgare L.) is an important cereal crop with high genome plasticity that is cultivated in all climatic zones. Traditionally, barley grain is used for animal feed, malting, brewing, and food production. Depending on the end-use product, there are individual requirements for the quality traits of barley grain, particularly for raw starch and protein contents. This study evaluates a collection of 406 two-rowed spring barley accessions, comprising cultivars and lines from the USA, Kazakhstan, Europe, and Africa, based on five grain quality traits (the contents of raw starch, protein, cellulose, and lipids, and grain test weight) over two years. The results of population structure analysis demonstrate the significant impact of geographical origin on the formation of subclusters in the studied population. It was also found that the environment significantly affects grain quality traits. Heat and drought stresses, particularly during grain filling, led to higher protein and lower starch contents. A genome-wide association study (GWAS) using a multiple-locus mixed linear model (MLMM) allowed for the identification of 26 significant quantitative trait loci (QTLs) for the five studied grain quality traits. Among them, 17 QTLs were found to be positioned close to known genes and previously reported QTLs for grain quality in the scientific literature. Most of the identified candidate genes were dehydration stress and flowering genes, confirming that exposure to heat and drought stresses during grain filling may lead to dramatic changes in grain quality traits, including lower starch and higher protein contents. Nine QTLs were presumably novel and could be used for gene mining and breeding activities, including marker-assisted selection to improve grain quality parameters. Full article
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops)
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