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Agronomy
Special Issues
Genetic Dissection and Improvement of Crop Traits
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Genetic Dissection and Improvement of Crop Traits

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

Deadline for manuscript submissions: closed (31 May 2024) | Viewed by 11347

Special Issue Editors

Dr. Hongwei Zhang

E-Mail Website
Guest Editor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
Interests: QTL mapping and cloning; genomic prediction; regulatory network
Dr. Riliang Gu

E-Mail Website
Guest Editor
Centor of Seed Science and Technology, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
Interests: genotype; best linear unbiased prediction; breeding value
Special Issues, Collections and Topics in MDPI journals
Dr. Kun Li

E-Mail Website
Guest Editor
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: genetics, germplasm, maize breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Xuehai Zhang

E-Mail Website
Guest Editor
College of Agronomy, Henan Agricultural University, Zhengzhou, China
Interests: plant genetics

Special Issue Information

Dear Colleagues,

With the advancements of various biotechnology tools, great breakthroughs in the dissection of crop traits are expected in the next few years. The publicly available functional markers and genes further boost the prediction and improvement of crop traits.

This Special Issue aims to provide a platform for crop researchers to discuss the progress of crop dissection and improvement, and to share their interesting research stories on a wide spectrum of cutting-edge research topics, which include but are not limited to:

Genetic dissection of various traits, including QTL mapping and genome-wide association;
Genomic prediction methods, models, and cases;
QTL introgression and evaluation;
Genotypic by environment interactions;
Omic-based analysis of variations of crop traits;
Mining natural alleles and creating/editing favorable alleles of functional genes;
The influences of functional genes on crop traits;
Physiological investigation of crop traits.


We welcome articles, reviews, methods, techniques, and opinions on the above-mentioned topics.

Dr. Hongwei Zhang
Dr. Riliang Gu
Dr. Kun Li
Dr. Xuehai Zhang
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

  • omic data
  • crop traits
  • genetic dissection
  • genomic prediction
  • functional genes

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Published Papers (6 papers)

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Research

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11 pages, 862 KiB  
Article
Fine-Mapping and Candidate Gene Analysis of qSERg-1b from O. glumaepatula to Improve Stigma Exsertion Rate in Rice
by Lixia Cao, Juncheng Dan, Xiaohui Li, Quanya Tan, Shaodi Zhang, Ruifeng Song and Xuelin Fu
Agronomy 2024, 14(2), 323; https://doi.org/10.3390/agronomy14020323 - 1 Feb 2024
Cited by 1 | Viewed by 1160
Abstract
The stigma exsertion rate (SER) is one of the important factors affecting the seed production of hybrid rice. In the genus Oryza, wild rice species usually show higher SERs than cultivars. We previously identified one novel SER-QTL, qSERg-1b, from the single-segment [...] Read more.
The stigma exsertion rate (SER) is one of the important factors affecting the seed production of hybrid rice. In the genus Oryza, wild rice species usually show higher SERs than cultivars. We previously identified one novel SER-QTL, qSERg-1b, from the single-segment substitution line (SSSL) SG22 of O. glumaepatula. In this study, qSERg-1b was fine-mapped by developing the secondary SSSLs (s-SSSLs) of SG22 and substitution mapping among the s-SSSLs. A total of 11 s-SSSLs were developed and used for qSERg-1b fine-mapping. As a result, qSERg-1b was narrowed down to the 122.59 kb physical region between InDel markers M01 and M49. There were 19 genes annotated in both O. glumaepatula and the HJX74 genomes at the qSERg-1b interval. Based on the genome re-sequencing of SG22 and HJX74, and the expression levels of the annotated functional genes, multiple nucleotide variations were found in LOC_Os01g53630, LOC_Os01g53680, and LOC_Os01g53710, including base substitutions and insertions/deletions of the genes, and they also showed significant differences in expression levels between SG22 and HJX74. Therefore, LOC_Os01g53630, LOC_Os01g53680, and LOC_Os01g53710 were selected as the most possible candidate genes of qSERg-1b for further validation. The above results laid an important foundation for qSERg-1b cloning and provided valuable resources for molecular breeding of SER in rice. Full article
(This article belongs to the Special Issue Genetic Dissection and Improvement of Crop Traits)
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21 pages, 4809 KiB  
Article
PEG-6000 Priming Improves Aged Soybean Seed Vigor via Carbon Metabolism, ROS Scavenging, Hormone Signaling, and Lignin Synthesis Regulation
by Yongqiang Wang, Enqiang Zhou, Mengnan Yao, Dong Xue, Na Zhao, Yao Zhou, Bo Li, Kaihua Wang, Yamei Miao, Chunyan Gu, Xuejun Wang and Libin Wei
Agronomy 2023, 13(12), 3021; https://doi.org/10.3390/agronomy13123021 - 8 Dec 2023
Cited by 1 | Viewed by 1709
Abstract
Seed priming, a valuable seed pretreatment method widely employed in agricultural production, counteracts the decline in seed vigor attributed to aging and deterioration. However, PEG priming effectively enhances the vigor of aged soybean seeds. In this study, “TONGDOU13” soybean seeds were subjected to [...] Read more.
Seed priming, a valuable seed pretreatment method widely employed in agricultural production, counteracts the decline in seed vigor attributed to aging and deterioration. However, PEG priming effectively enhances the vigor of aged soybean seeds. In this study, “TONGDOU13” soybean seeds were subjected to PEG-6000 priming at varying concentrations (10%, 20%, 30%, 40%) for three different durations (12 h, 24 h, 36 h). The results showed that a 24 h priming with 30% PEG-6000 significantly enhances the vigor of aged soybean seeds. To elucidate the mechanism underlying the heightened vigor resulting from PEG-6000 priming, we employed transcriptome sequencing and physiological–biochemical tests. Transcriptome sequencing analysis showed the significant down-regulation of carbon metabolism-related genes post PEG-6000 priming, which facilitated energetically efficient germination. Five peroxidase-encoding genes displayed significant up-regulation, promoting the conversion of coumaryl alcohol to hydroxy-phenyl lignin, a probable catalyst for augmented seed vigor. SOD and GST genes were significantly up-regulated, enhancing the scavenging ability of reactive oxygen species (ROS). The concurrent up-regulation of brassinolide (BR) and auxin (IAA) signals countered ABA signaling, thereby promoting aged seed germination. Further investigation included the measurements of antioxidant enzyme activity, hormone levels, and lignin content. Notably, primed aged seeds exhibited enhanced ROS scavenging ability, and increased lignin, BR, and IAA contents. Therefore, PEG priming may improve aged soybean seed vigor through the co-regulation of carbon metabolism, ROS scavenging, hormone signaling, and lignin synthesis. This study will be vital for preserving germplasm resources and reutilizing aged soybean seeds. Full article
(This article belongs to the Special Issue Genetic Dissection and Improvement of Crop Traits)
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15 pages, 3979 KiB  
Article
Historical Trends Analysis of Main Agronomic Traits in South China Inbred Indica Rice Varieties since Dwarf Breeding
by Xiaomin Feng, Ying Zhao, Wenlong Nie, Qiang Zhang, Zhixia Liu, Yijun Jiang, Kai Chen, Ning Yu, Xin Luan, Wenlong Li, Miaomiao Shan, Jianlong Xu and Qingshan Lin
Agronomy 2023, 13(8), 2159; https://doi.org/10.3390/agronomy13082159 - 17 Aug 2023
Viewed by 1247
Abstract
Studying the evolutionary patterns of rice agronomic traits in South China and analyzing the characteristics of rice improvement can provide insights into the developmental trajectory of rice breeding in South China and can guide further enhancement of variety yield. In this study, widely [...] Read more.
Studying the evolutionary patterns of rice agronomic traits in South China and analyzing the characteristics of rice improvement can provide insights into the developmental trajectory of rice breeding in South China and can guide further enhancement of variety yield. In this study, widely promoted varieties and core parents developed through dwarf breeding in the southern region, as well as landraces, were collected and planted in three different ecological regions. A total of 18 agronomic traits were investigated related to heading date, plant type, panicle type, grain type, and yield, and multiple comparisons, a correlation analysis, and a path analysis were conducted. The results indicate that dwarf breeding has significantly increased the yield of inbred indica rice varieties in South China. However, a reduction in plant height has also resulted in a reduction in flag leaf, shorter panicles, and decreased biomass, which have led to metabolic source and storage capacity deficiencies and limited yield potential. To address these limitations, breeders have employed strategies such as increasing flag leaf width, spikelet density, number of primary branches, and grain number per panicle. These measures have led to a gradual increase in yield. Additionally, starting from the 1980s, high-quality rice breeding has been pursued in South China, resulting in slender grain shape and reduced thousand grain weight. Given that total grain number per panicle has already increased significantly and the thousand grain weight cannot be reduced further, enhancing the effective tiller number, which decreases year by year, becomes an important approach to increasing the yield of inbred indica rice varieties in South China. Full article
(This article belongs to the Special Issue Genetic Dissection and Improvement of Crop Traits)
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11 pages, 1817 KiB  
Article
Over-Expression of ZmIAA29, an AUX/IAA Transcription Factor, Improved Maize Flowering Time
by Chenhui Ma, Kuntai Dang, Qiankun Xie, Javed Hussain Sahito, Baiyu Yuan, Jiong Wan, Xiaoqian Qiu, Jiawen Zhao, Yanan Lin, Shujun Meng, Liqin Mu, Dong Ding, Huili Yang, Yadong Xue, Xiaoyang Chen, Xuehai Zhang and Jihua Tang
Agronomy 2023, 13(8), 2028; https://doi.org/10.3390/agronomy13082028 - 31 Jul 2023
Cited by 4 | Viewed by 1691
Abstract
Maize is one of the most important food and feed crops in China due to the high demand for its use by both humans and animals. The Huang-Huai-Hai region is a major maize cultivation area in China, and the special cropping rotation system [...] Read more.
Maize is one of the most important food and feed crops in China due to the high demand for its use by both humans and animals. The Huang-Huai-Hai region is a major maize cultivation area in China, and the special cropping rotation system of wheat and maize requires a suitable reproductive period for maize. The AUX/IAA and ARF transcription factors are two key genes that regulate auxin signals in plants, which play an important role during the process of auxin regulation in plant growth and development. In this study, we obtained two overexpressed lines of ZmIAA29 belonging to the AUX/IAA transcription factor family. Compared with the Wide type, the overexpressed strains of ZmIAA29 were significantly regulated in maize during the flowering time and had increased ear weight. Moreover, ZmIAA29 was assayed via the yeast two-hybrid and BiLUC systems for interaction, and the results showed that ZmIAA29 interacted with several ZmARF transcription factors. Furthermore, RNA-seq and DAP-seq analysis revealed that ZmIAA29 regulates maize growth and development by influencing pathways such as those for plant signal transduction and the key genes related to maize flowering. Taken together, our results suggest that ZmIAA29 plays a key role in the development of maize flowering. This study provides new insight for better understanding the combined regulation of the AUX/IAA and ARF transcription factors during flowering time in maize. Full article
(This article belongs to the Special Issue Genetic Dissection and Improvement of Crop Traits)
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13 pages, 3327 KiB  
Article
Genome-Wide Association Study for Fusarium Head Blight Resistance in Common Wheat from China
by Chaonan Shi, Huaiyu Chao, Xiaonan Sun, Yongqiang Suo, Zeyu Chen, Zhikang Li, Lin Ma, Jiaqi Li, Yan Ren, Wei Hua, Caixia Lan and Feng Chen
Agronomy 2023, 13(7), 1712; https://doi.org/10.3390/agronomy13071712 - 26 Jun 2023
Cited by 1 | Viewed by 2199
Abstract
As a devastating wheat disease, Fusarium head blight (FHB) causes large losses in yield and quality. The purpose of this study was to detect the genetic loci for FHB resistance based on a genome-wide association study (GWAS) using two panels genotyped by the [...] Read more.
As a devastating wheat disease, Fusarium head blight (FHB) causes large losses in yield and quality. The purpose of this study was to detect the genetic loci for FHB resistance based on a genome-wide association study (GWAS) using two panels genotyped by the Wheat 660 K SNP array and Wheat 90 K SNP array. Phenotypic investigation results showed that 43.6–51.6% of the test varieties showed an infection type of more than 3, indicating that substantial improvement in the level of resistance was urgently required. GWAS detected 1264 SNPs associated with FHB response distributed on all wheat chromosomes. Fourteen QTL were stably detected in two environments. gFHB-1B (582.9~607.9 Mb on chromosome 1B) and gFHB-5A (577.9~596.5 Mb on 5A) were two novel resistance loci that were detected in two wheat panels. Haplotype analysis of both gFHB-1B and gFHB-5A indicated that varieties with gFHB-1B_R and gFHB-5A_R had consistently less FHB than varieties carrying a one or no resistance QTL. The application frequency of the FHB-resistant alleles gFHB-1B and gFHB-5A showed a gradually decreasing trend in FHB resistance breeding. This study identified new genetic loci for the control of FHB and provides useful information for marker-assisted selection in wheat FHB resistance. Full article
(This article belongs to the Special Issue Genetic Dissection and Improvement of Crop Traits)
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Review

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30 pages, 2515 KiB  
Review
Genetic and Genomic Pathways to Improved Wheat (Triticum aestivum L.) Yields: A Review
by Zaid Chachar, Lina Fan, Sadaruddin Chachar, Nazir Ahmed, Mehar-un-Nisa Narejo, Naseer Ahmed, Ruiqiang Lai and Yongwen Qi
Agronomy 2024, 14(6), 1201; https://doi.org/10.3390/agronomy14061201 - 1 Jun 2024
Viewed by 2232
Abstract
Wheat (Triticum aestivum L.) is a fundamental crop essential for both human and animal consumption. Addressing the challenge of enhancing wheat yield involves sophisticated applications of molecular genetics and genomic techniques. This review synthesizes current research identifying and characterizing pivotal genes that [...] Read more.
Wheat (Triticum aestivum L.) is a fundamental crop essential for both human and animal consumption. Addressing the challenge of enhancing wheat yield involves sophisticated applications of molecular genetics and genomic techniques. This review synthesizes current research identifying and characterizing pivotal genes that impact traits such as grain size, number, and weight, critical factors influencing overall yield. Key genes including TaSPL17, ABP7, TaGNI, TaCKX6, TaGS5, TaDA1, WAPO1, TaRht1, TaTGW-7A, TaGW2, TaGS5-3A, TaSus2-2A, TaSus2-2B, TaSus1-7A, and TaSus1-7B are examined for their roles in these traits. The review also explores genes responsive to environmental changes, which are increasingly significant under current climate variability. Multi-trait regulatory genes and quantitative trait loci (QTLs) that contribute to these traits are discussed, highlighting their dual influences on grain size and yield. Furthermore, the paper underscores the utility of emerging technologies such as CRISPR/Cas9, Case13, and multi-omics approaches. These innovations are instrumental for future discoveries and are poised to revolutionize wheat breeding by enabling precise genetic enhancements. Facing unprecedented challenges from climate change, the identification and utilization of these candidates is crucial. This review aims to be a comprehensive resource for researchers, providing an integrative understanding of complex traits in wheat and proposing new avenues for research and crop improvement strategies. Full article
(This article belongs to the Special Issue Genetic Dissection and Improvement of Crop Traits)
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