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Agronomy
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Analysis of Complex Traits and Molecular Selection in Annual Crops—2nd...
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Analysis of Complex Traits and Molecular Selection in Annual Crops—2nd Edition

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 2025) | Viewed by 4726

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,

Following the first edition of this Special Issue, "Analysis of Complex Traits and Molecular Selection in Annual Crops", in Agronomy, the Editorial Office would like to launch a second edition. The subject, the editorial team, and the submission process will remain the same.

The agronomic traits of crops are some of the most pressing issues in agricultural production. Analyses of complex agronomic traits, such as crop yield, quality and stress resistance, molecular selection, and the construction as well as mining of complex relationship networks between crop genes and agronomic traits, represent the frontiers of and hot issues in crop research. The 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 that analyzes complex agronomic traits. With the development of high-throughput sequencing technology, we can comprehensively and systematically understand the compositions 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 in addition to 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

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Related Special Issue

Published Papers (3 papers)

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Research

11 pages, 1245 KiB  
Article
Quantitative Trait Loci Mapping and Candidate Gene Analysis for Fiber Quality Traits in Upland Cotton
by Xiaoyun Jia, Hongxia Zhao, Jijie Zhu, Shijie Wang, Miao Li and Guoyin Wang
Agronomy 2024, 14(8), 1719; https://doi.org/10.3390/agronomy14081719 - 5 Aug 2024
Viewed by 1310
Abstract
Superior fiber quality is one of the most important objectives in cotton breeding. To detect the genetic basis underlying fiber quality, an F2 population containing 413 plants was constructed by crossing Jifeng 914 and Jifeng 173, both of which have superior fiber quality, [...] Read more.
Superior fiber quality is one of the most important objectives in cotton breeding. To detect the genetic basis underlying fiber quality, an F2 population containing 413 plants was constructed by crossing Jifeng 914 and Jifeng 173, both of which have superior fiber quality, with Jifeng 173 being better. Five fiber quality traits were investigated in the F2, F2:3, F2:4, and F2:5 populations. Quantitative trait loci (QTL) mapping was conducted based on a high-density genetic map containing 11,488 single nucleotide polymorphisms (SNPs) and spanning 4202.12 cM in length. Transgressive segregation patterns and complex correlations in the five tested traits were observed. A total of 108 QTLs were found, including 13 major effect QTLs that contributed more than 10% toward phenotypic variation (PV) and 9 stable QTLs that could be repeatedly mapped in different generations. Chromosome A7 contained 12 QTL, ranking the first. No QTL was found on chromosomes D1 and D11. Two QTLs could be repeatedly detected in three populations, including qFL-D3-2 in F2, F2:4, and F2:5 with 9.18–21.45% of PV and qFS-A11-1 in F2:3, F2:4, and F2:5 with 6.05–10.41% of PV. Another seven stable QTLs could be detected in two populations, including four major effect QTLs: qFL-A12-3, qFS-D10-2, qMC-D6-2, and qMC-D8-1. Fourteen QTL-overlapping regions were found, which might explain the complex correlations among the five phenotypic traits. Four regions on chromosome A11, D3, D6, and D10 covered by both stable and major effect QTLs are promising for further fine mapping. The genomic regions of the two QTLs detected in three populations and the four major effect QTLs contain 810 genes. Gene functional analysis revealed that the annotated genes are mainly involved in protein binding and metabolic pathways. Fifteen candidate genes in the qFL-D3-2 region are highly expressed in fiber or ovules during fiber initiation, elongation, secondary cell wall thickening, or maturation stages. qRT-PCR revealed that Ghir_D03G005440.1 and Ghir_D03G011310.1 may play a role in promoting fiber initiation, while Ghir_D03G006470.1 may be beneficial for promoting fiber elongation. This study provides more information for revealing the molecular genetic basis underlying cotton fiber quality. Full article
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops—2nd Edition)
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22 pages, 7299 KiB  
Article
Novel QTL Hotspots for Barley Flowering Time, Plant Architecture, and Grain Yield
by Yuliya Genievskaya, Vladimir Chudinov, Saule Abugalieva and Yerlan Turuspekov
Agronomy 2024, 14(7), 1478; https://doi.org/10.3390/agronomy14071478 - 8 Jul 2024
Cited by 2 | Viewed by 1284
Abstract
Barley (Hordeum vulgare L.) is one of the oldest cultivated grains and remains a significant crop globally. Barley breeders focus on developing high-yield cultivars resistant to biotic and abiotic stresses. Barley’s flowering time, regulated genetically and by environmental stimuli, significantly impacts all [...] Read more.
Barley (Hordeum vulgare L.) is one of the oldest cultivated grains and remains a significant crop globally. Barley breeders focus on developing high-yield cultivars resistant to biotic and abiotic stresses. Barley’s flowering time, regulated genetically and by environmental stimuli, significantly impacts all of its agronomic traits, including the grain yield and plant architecture. This study aimed to detect the quantitative trait loci (QTLs) affecting these traits in 273 two-row spring barley accessions from the USA, Kazakhstan, Europe, and the Middle East across two regions of Kazakhstan, evaluating their impact on grain yield. Genotypic data were obtained from 26,529 segregating single-nucleotide polymorphisms (SNPs), and field trial data for 273 accessions, which were obtained for six traits (heading time, maturity time, vegetation period, plant height, peduncle length, and grain yield) in two regions of Kazakhstan over three growth years. As a result of a genome-wide association study (GWAS), 95 QTLs were identified for 6 agronomic traits, including 58 QTLs linked with candidate genes and/or QTLs. The remaining 37 QTLs were putatively novel, with 13 of them forming 3 QTL hotspots on chromosomes 1H (5 QTLs in the interval of 13.4–41.4 Mbp), 3H (4 QTLs in 608.6–624.9 Mbp), and 6H (4 QTLs in 553.8–572.8 Mbp). These hotspots were pleiotropic, and targeting these regions would allow breeders to enhance multiple yield-associated traits. Full article
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops—2nd Edition)
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16 pages, 18691 KiB  
Article
Comprehensive Genome-Wide Investigation and Transcriptional Regulation of the DHHC Gene Family in Cotton Seed and Fiber Development
by Saimire Silaiyiman, Qinyue Zheng, Yutao Wang, Lejun Ouyang, Zhishan Guo, Jieli Yu, Rong Chen, Rui Peng and Chao Shen
Agronomy 2024, 14(6), 1214; https://doi.org/10.3390/agronomy14061214 - 4 Jun 2024
Viewed by 1593
Abstract
Protein palmitoylation, the most common and the only reversible post-translational lipid modification following protein translation, plays a pivotal role in the biochemical and physiological processes of both animals and plants. DHHC proteins, enriched with DHHC (Asp-His-His-Cys) domains, serve as catalyst for protein palmitoylation. [...] Read more.
Protein palmitoylation, the most common and the only reversible post-translational lipid modification following protein translation, plays a pivotal role in the biochemical and physiological processes of both animals and plants. DHHC proteins, enriched with DHHC (Asp-His-His-Cys) domains, serve as catalyst for protein palmitoylation. However, research on DHHC in cotton remains scarce. This study conducted a systematic characterization and bioinformatics analysis on G. arboreum, G. raimondii, G. hirsutum, and G. barbadense, detecting 38, 37, 74, and 74 DHHC genes, respectively. Phylogenetic analysis categorized the DHHC gene family into six subgroups, consistent with previous evolutionary studies in Arabidopsis and rice. A further examination of protein structure revealed a correlation between genetic relatedness, structural similarity, and functional identity. Cis-element analysis identified elements predominantly associated with light response, stress, growth and development, and plant hormones. The integration of cotton seed development transcriptome, tissue expression pattern analysis, and population transcriptome data collectively suggests that Ghir_A05G027650 and Ghir_D05G027670 are promising candidate genes influencing seed development in upland cotton. Conversely, Gbar_A04G010750 and Gbar_A12G020520 emerge as potential candidates affecting both seed and fiber development in sea island cotton. These findings lay down a theoretical foundation for delving into the functional diversity of DHHC genes in cotton, thereby paving the way for the development of new breeding strategies and the optimization of cotton seed and fiber production, ultimately contributing to improved crop yield and quality. Full article
(This article belongs to the Special Issue Analysis of Complex Traits and Molecular Selection in Annual Crops—2nd Edition)
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